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Diotallevi A, Bruno F, Castelli G, Persico G, Buffi G, Ceccarelli M, Ligi D, Mannello F, Vitale F, Magnani M, Galluzzi L. Transcriptional signatures in human macrophage-like cells infected by Leishmania infantum, Leishmania major and Leishmania tropica. PLoS Negl Trop Dis 2024; 18:e0012085. [PMID: 38578804 PMCID: PMC11023634 DOI: 10.1371/journal.pntd.0012085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/17/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND In the Mediterranean basin, three Leishmania species have been identified: L. infantum, L. major and L. tropica, causing zoonotic visceral leishmaniasis (VL), zoonotic cutaneous leishmaniasis (CL) and anthroponotic CL, respectively. Despite animal models and genomic/transcriptomic studies provided important insights, the pathogenic determinants modulating the development of VL and CL are still poorly understood. This work aimed to identify host transcriptional signatures shared by cells infected with L. infantum, L. major, and L. tropica, as well as specific transcriptional signatures elicited by parasites causing VL (i.e., L. infantum) and parasites involved in CL (i.e., L. major, L. tropica). METHODOLOGY/PRINCIPAL FINDINGS U937 cells differentiated into macrophage-like cells were infected with L. infantum, L. major and L. tropica for 24h and 48h, and total RNA was extracted. RNA sequencing, performed on an Illumina NovaSeq 6000 platform, was used to evaluate the transcriptional signatures of infected cells with respect to non-infected cells at both time points. The EdgeR package was used to identify differentially expressed genes (fold change > 2 and FDR-adjusted p-values < 0.05). Then, functional enrichment analysis was employed to identify the enriched ontology terms in which these genes are involved. At 24h post-infection, a common signature of 463 dysregulated genes shared among all infection conditions was recognized, while at 48h post-infection the common signature was reduced to 120 genes. Aside from a common transcriptional response, we evidenced different upregulated functional pathways characterizing L. infantum-infected cells, such as VEGFA-VEGFR2 and NFE2L2-related pathways, indicating vascular remodeling and reduction of oxidative stress as potentially important factors for visceralization. CONCLUSIONS The identification of pathways elicited by parasites causing VL or CL could lead to new therapeutic strategies for leishmaniasis, combining the canonical anti-leishmania compounds with host-directed therapy.
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Affiliation(s)
- Aurora Diotallevi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Federica Bruno
- Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), OIE Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia A Mirri, Palermo, Italy
| | - Germano Castelli
- Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), OIE Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia A Mirri, Palermo, Italy
| | - Giuseppe Persico
- Department of Experimental Oncology, IRCCS, European Institute of Oncology, Milan, Italy
| | - Gloria Buffi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Marcello Ceccarelli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Daniela Ligi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Ferdinando Mannello
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Fabrizio Vitale
- Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), OIE Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia A Mirri, Palermo, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Luca Galluzzi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
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Fernandes JCR, Muxel SM, López-Gonzálvez MA, Barbas C, Floeter-Winter LM. Early Leishmania infectivity depends on miR-372/373/520d family-mediated reprogramming of polyamines metabolism in THP-1-derived macrophages. Sci Rep 2024; 14:996. [PMID: 38200138 PMCID: PMC10781704 DOI: 10.1038/s41598-024-51511-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024] Open
Abstract
Leishmania amazonensis is a protozoan that primarily causes cutaneous leishmaniasis in humans. The parasite relies on the amino acid arginine to survive within macrophages and establish infection, since it is a precursor for producing polyamines. On the other hand, arginine can be metabolized via nitric oxide synthase 2 (NOS2) to produce the microbicidal molecule nitric oxide (NO), although this mechanism does not apply to human macrophages since they lack NOS2 activity. MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at posttranscriptional levels. Our previous work showed that mmu-miR-294 targets Nos2 favoring Leishmania survival in murine macrophages. Here, we demonstrate that human macrophages upregulate the hsa-miR-372, hsa-miR-373, and hsa-miR-520d, which present the same seed sequence as the murine mmu-miR-294. Inhibition of the miR-372 impaired Leishmania survival in THP-1 macrophages and the effect was further enhanced with combinatorial inhibition of the miR-372/373/520d family, pointing to a cooperative mechanism. However, this reduction in survival is not caused by miRNA-targeting of NOS2, since the seed-binding motif found in mice is not conserved in the human 3'UTR. Instead, we showed the miR-372/373/520d family targeting the macrophage's main arginine transporter SLC7A2/CAT2 during infection. Arginine-related metabolism was markedly altered in response to infection and miRNA inhibition, as measured by Mass Spectrometry-based metabolomics. We found that Leishmania infection upregulates polyamines production in macrophages, as opposed to simultaneous inhibition of miR-372/373/520d, which decreased putrescine and spermine levels compared to the negative control. Overall, our study demonstrates miRNA-dependent modulation of polyamines production, establishing permissive conditions for intracellular parasite survival. Although the effector mechanisms causing host cell immunometabolic adaptations involve various parasite and host-derived signals, our findings suggest that the miR-372/373/520d family may represent a potential target for the development of new therapeutic strategies against cutaneous leishmaniasis.
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Affiliation(s)
- J C R Fernandes
- Instituto de Medicina Tropical da Faculdade de Medicina, Universidade de São Paulo (IMT-FMUSP), São Paulo, Brazil
- Instituto de Biociências, Universidade de São Paulo (IB-USP), São Paulo, Brazil
| | - S M Muxel
- Instituto de Ciências Biomédicas, Universidade de São Paulo (ICB-USP), São Paulo, Brazil
| | - M A López-Gonzálvez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain
| | - C Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain
| | - L M Floeter-Winter
- Instituto de Biociências, Universidade de São Paulo (IB-USP), São Paulo, Brazil.
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Moradimotlagh A, Chen S, Koohbor S, Moon KM, Foster LJ, Reiner N, Nandan D. Leishmania infection upregulates and engages host macrophage Argonaute 1, and system-wide proteomics reveals Argonaute 1-dependent host response. Front Immunol 2023; 14:1287539. [PMID: 38098491 PMCID: PMC10720368 DOI: 10.3389/fimmu.2023.1287539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/26/2023] [Indexed: 12/17/2023] Open
Abstract
Leishmania donovani, an intracellular protozoan parasite, is the causative agent of visceral leishmaniasis, the most severe form of leishmaniasis in humans. It is becoming increasingly clear that several intracellular pathogens target host cell RNA interference (RNAi) pathways to promote their survival. Complexes of Argonaute proteins with small RNAs are core components of the RNAi. In this study, we investigated the potential role of host macrophage Argonautes in Leishmania pathogenesis. Using Western blot analysis of Leishmania donovani-infected macrophages, we show here that Leishmania infection selectively increased the abundance of host Argonaute 1 (Ago1). This increased abundance of Ago1 in infected cells also resulted in higher levels of Ago1 in active Ago-complexes, suggesting the preferred use of Ago1 in RNAi in Leishmania-infected cells. This analysis used a short trinucleotide repeat containing 6 (TNRC6)/glycine-tryptophan repeat protein (GW182) protein-derived peptide fused to Glutathione S-transferase as an affinity matrix to capture mature Ago-small RNAs complexes from the cytosol of non-infected and Leishmania-infected cells. Furthermore, Ago1 silencing significantly reduced intracellular survival of Leishmania, demonstrating that Ago1 is essential for Leishmania pathogenesis. To investigate the role of host Ago1 in Leishmania pathogenesis, a quantitative whole proteome approach was employed, which showed that expression of several previously reported Leishmania pathogenesis-related proteins was dependent on the level of macrophage Ago1. Together, these findings identify Ago1 as the preferred Argonaute of RNAi machinery in infected cells and a novel and essential virulence factor by proxy that promotes Leishmania survival.
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Affiliation(s)
- Atieh Moradimotlagh
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Stella Chen
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sara Koohbor
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J. Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Neil Reiner
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Devki Nandan
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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Palacios G, Diaz-Solano R, Valladares B, Dorta-Guerra R, Carmelo E. Evolving immunometabolic response to the early Leishmania infantum infection in the spleen of BALB/c mice described by gene expression profiling. Acta Trop 2023; 247:107005. [PMID: 37619900 DOI: 10.1016/j.actatropica.2023.107005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/27/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
Transcriptional analysis is a useful approximation towards the identification of global changes in host-pathogen interaction, in order to elucidate tissue-specific immune responses that drive the immunopathology of the disease. For this purpose, expression of 223 genes involved in innate and adaptive immune response, lipid metabolism, prostaglandin synthesis, C-type lectin receptors and MAPK signaling pathway, among other processes, were analyzed during the early infection in spleens of BALB/c mice infected by Leishmania infantum. Our results highlight the activation of immune responses in spleen tissue as early as 1 day p.i., but a mixed pro-inflammatory and regulatory response at day 10 p.i., failing to induce an effective response towards control of Leishmania infection in the spleen. This ineffective response is coupled to downregulation of metabolic markers relevant for pathways related to icosanoid biosynthesis, adipocytokine signaling or HIF-1 signaling, among others. Interestingly, the over-representation of processes related to immune response, revealed Il21 as a potential early biomarker of L. infantum infection in the spleen. These results provide insights into the relationships between immune and metabolic responses at transcriptional level during the first days of infection in the L. infantum-BALB/c experimental model, revealing the deregulation of many important pathways and processes crucial for parasitic control in infected tissues.
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Affiliation(s)
- Génesis Palacios
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n (Tenerife), La Laguna 38200, Spain
| | - Raquel Diaz-Solano
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n (Tenerife), La Laguna 38200, Spain
| | - Basilio Valladares
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n (Tenerife), La Laguna 38200, Spain; Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, (Tenerife), La Laguna 38200, Spain
| | - Roberto Dorta-Guerra
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n (Tenerife), La Laguna 38200, Spain; Departamento de Matemáticas, Estadística e Investigación Operativa, Facultad de Ciencias, Universidad de La Laguna, (Tenerife), La Laguna 38200, Spain
| | - Emma Carmelo
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n (Tenerife), La Laguna 38200, Spain; Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, (Tenerife), La Laguna 38200, Spain.
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Chang Y, Li S, Wang L, Wang K, Li J, Li X, Jian F, Wang R, Zhang S, Zhang L. Micro-RNA expression profile of BALB/c mouse glandular stomach in the early phase of Cryptosporidium muris infection. Exp Parasitol 2023; 253:108603. [PMID: 37633513 DOI: 10.1016/j.exppara.2023.108603] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023]
Abstract
Cryptosporidiosis is a zoonotic disease in humans and animals that is caused by infection with the oocysts of Cryptosporidium. MicroRNAs (miRNAs) are important players in regulating the innate immune response against parasitic infection. Public miRNAs data for studying pathogenic mechanisms of cryptosporidiosis, particularly in natural hosts, are scarce. Here, we compared miRNA profiles of the glandular stomach of C. muris-infected and uninfected BALB/c mice using microarray sequencing. A total of 10 miRNAs (including 3 upregulated and 7 downregulated miRNAs) with significant differential expression (|FC| ≥ 2 and P value < 0.05) were identified in the glandular stomach of BALB/c mice 8 h after infection with C. muris. MiRWalk and miRDB online bioinformatics tools were used to predict the target genes of differentially expressed miRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to annotate the target genes. GO analysis indicate that gene transcription-related and ion transport-related GO terms were significantly enriched. In addition, the KEGG analyses showed that the target genes were strongly related to diverse types of tumor disease progression and anti-pathogen immunity pathways. In the current study, we firstly report changes in miRNA expression profiles in the glandular stomach of BALB/c mice at the early phase of C. muris invasion. This dysregulation in miRNA expression may contribute to our understanding of cryptosporidiosis pathology. This study provides a new perspective on the miRNA regulatory mechanisms of cryptosporidiosis, which may help in the development of effective control strategies against this pathogen.
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Affiliation(s)
- Yankai Chang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, 450046, China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, Henan, 450046, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, Henan, 450046, China.
| | - Songrui Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, 450046, China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, Henan, 450046, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, Henan, 450046, China.
| | - Luyang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, 450046, China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, Henan, 450046, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, Henan, 450046, China.
| | - Ke Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, 450046, China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, Henan, 450046, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, Henan, 450046, China.
| | - Junqiang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, 450046, China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, Henan, 450046, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, Henan, 450046, China.
| | - Xiaoying Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, 450046, China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, Henan, 450046, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, Henan, 450046, China.
| | - Fuchun Jian
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, 450046, China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, Henan, 450046, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, Henan, 450046, China.
| | - Rongjun Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, 450046, China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, Henan, 450046, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, Henan, 450046, China.
| | - Sumei Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, 450046, China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, Henan, 450046, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, Henan, 450046, China.
| | - Longxian Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, 450046, China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou, Henan, 450046, China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, Henan, 450046, China.
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Karagiannis K, Gannavaram S, Verma C, Pacheco-Fernandez T, Bhattacharya P, Nakhasi HL, Satoskar AR. Dual-scRNA-seq analysis reveals rare and uncommon parasitized cell populations in chronic L. donovani infection. Cell Rep 2023; 42:113097. [PMID: 37682713 DOI: 10.1016/j.celrep.2023.113097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 06/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Although phagocytic cells are documented targets of Leishmania parasites, it is unclear whether other cell types can be infected. Here, we use unbiased single-cell RNA sequencing (scRNA-seq) to simultaneously analyze host cell and Leishmania donovani transcriptomes to identify and annotate parasitized cells in spleen and bone marrow in chronically infected mice. Our dual-scRNA-seq methodology allows the detection of heterogeneous parasitized populations. In the spleen, monocytes and macrophages are the dominant parasitized cells, while megakaryocytes, basophils, and natural killer (NK) cells are found to be unexpectedly infected. In the bone marrow, the hematopoietic stem cells (HSCs) expressing phagocytic receptors FcγR and CD93 are the main parasitized cells. Additionally, we also detect parasitized cycling basal cells, eosinophils, and macrophages in chronically infected mice. Flow cytometric analysis confirms the presence of parasitized HSCs. Our unbiased dual-scRNA-seq method identifies rare, parasitized cells, potentially implicated in pathogenesis, persistence, and protective immunity, using a non-targeted approach.
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Affiliation(s)
| | - Sreenivas Gannavaram
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, USA
| | - Chaitenya Verma
- Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
| | | | - Parna Bhattacharya
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, USA
| | - Hira L Nakhasi
- Division of Emerging and Transfusion Transmitted Diseases, CBER, FDA, Silver Spring, MD, USA
| | - Abhay R Satoskar
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA.
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Venugopal G, Bird JT, Roys H, Bowlin A, Fry L, Byrum SD, Weinkopff T. BOTH THE INFECTION STATUS AND INFLAMMATORY MICROENVIRONMENT INDUCE TRANSCRIPTIONAL REMODELING IN MACROPHAGES IN MURINE LEISHMANIAL LESIONS. J Parasitol 2023; 109:200-210. [PMID: 37270767 DOI: 10.1645/22-94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023] Open
Abstract
Cutaneous leishmaniasis is caused by infection with the protozoan parasite Leishmania, which resides intracellularly in dermal macrophages (Mø), producing lesions. The skin lesions are characterized by proinflammatory cytokines and growth factors as well as inflammatory hypoxia, creating a stressful microenvironment for Mø. Of importance, not all Mø in lesions harbor parasites. To distinguish the influence of the parasite from the inflammatory microenvironment after Leishmania major (LM) infection on the Mø, we performed single-cell RNA sequencing and compared Mø associated with LM transcripts (or 'infected' Mø) with Mø not associated with LM transcripts (or 'bystander' Mø) within the lesions. Our findings show coordinated lysosomal expression and regulation signaling with increased cathepsin and H+-ATPase transcripts are upregulated in infected compared with bystander Mø. Additionally, eukaryotic initiation factor 2 (EIF2) signaling is downregulated in infected compared with bystander Mø, which includes many small and large ribosomal subunit (Rps and Rpl) transcripts being decreased in Mø harboring parasites. Furthermore, we also find EIF2 signaling including EIF, Rps, and Rpl transcripts being downregulated in bystander Mø compared with Mø from naïve skin. These data suggest that both the parasite and the inflammatory host microenvironment affect the transcription of ribosomal machinery in lesional Mø, thereby potentially affecting the ability of these cells to perform translation, protein synthesis, and thus function. Altogether, these results suggest that both the parasite and host inflammatory microenvironment independently drive transcriptional remodeling in Mø during LM infection in vivo.
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Affiliation(s)
- Gopinath Venugopal
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Jordan T Bird
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
- Arkansas Children's Research Institute, Little Rock, Arkansas 72202
| | - Hayden Roys
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Anne Bowlin
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Lucy Fry
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
- Arkansas Children's Research Institute, Little Rock, Arkansas 72202
| | - Tiffany Weinkopff
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
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Zaldívar-López S, Herrera-Uribe J, Bautista R, Jiménez Á, Moreno Á, Claros MG, Garrido JJ. Salmonella Typhimurium induces genome-wide expression and phosphorylation changes that modulate immune response, intracellular survival and vesicle transport in infected neutrophils. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 140:104597. [PMID: 36450302 DOI: 10.1016/j.dci.2022.104597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Salmonella Typhimurium is a food-borne pathogen that causes salmonellosis. When in contact with the host, neutrophils are rapidly recruited to act as first line of defense. To better understand the pathogenesis of this infection, we used an in vitro model of neutrophil infection to perform dual RNA-sequencing (both host and pathogen). In addition, and given that many pathogens interfere with kinase-mediated phosphorylation in host signaling, we performed a phosphoproteomic analysis. The immune response was overall diminished in infected neutrophils, mainly JAK/STAT and toll-like receptor signaling pathways. We found decreased expression of proinflammatory cytokine receptor genes and predicted downregulation of the mitogen-activated protein (MAPK) signaling pathway. Also, Salmonella infection inhibited interferons I and II signaling pathways by upregulation of SOCS3 and subsequent downregulation of STAT1 and STAT2. Additionally, phosphorylation of PSMC2 and PSMC4, proteasome regulatory proteins, was decreased in infected neutrophils. Cell viability and survival was increased by p53 signaling, cell cycle arrest and NFkB-proteasome pathways activation. Combined analysis of RNA-seq and phosphoproteomics also revealed inhibited vesicle transport mechanisms mediated by dynein/dynactin and exocyst complexes, involved in ER-to-Golgi transport and centripetal movement of lysosomes and endosomes. Among the overexpressed virulence genes from Salmonella we found potential effectors responsible of these dysregulations, such as spiC, sopD2, sifA or pipB2, all of them involved in intracellular replication. Our results suggest that Salmonella induces (through overexpression of virulence factors) transcriptional and phosphorylation changes that increases neutrophil survival and shuts down immune response to minimize host response, and impairing intracellular vesicle transport likely to keep nutrients for replication and Salmonella-containing vacuole formation and maintenance.
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Affiliation(s)
- Sara Zaldívar-López
- Grupo de Inmunogenómica y Patogénesis Molecular, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain.
| | - Juber Herrera-Uribe
- Grupo de Inmunogenómica y Patogénesis Molecular, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Rocío Bautista
- Plataforma Andaluza de Bioinformática, Universidad de Málaga, Málaga, Spain
| | - Ángeles Jiménez
- Grupo de Inmunogenómica y Patogénesis Molecular, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Ángela Moreno
- Grupo de Inmunogenómica y Patogénesis Molecular, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - M Gonzalo Claros
- Plataforma Andaluza de Bioinformática, Universidad de Málaga, Málaga, Spain; Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga, Spain
| | - Juan J Garrido
- Grupo de Inmunogenómica y Patogénesis Molecular, UIC Zoonosis y Enfermedades Emergentes ENZOEM, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
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9
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Dual RNA sequencing of group B Streptococcus-infected human monocytes reveals new insights into host-pathogen interactions and bacterial evasion of phagocytosis. Sci Rep 2023; 13:2137. [PMID: 36747074 PMCID: PMC9902490 DOI: 10.1038/s41598-023-28117-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/13/2023] [Indexed: 02/08/2023] Open
Abstract
Streptococcus agalactiae, also known as Group B Streptococcus (GBS) is a frequent cause of infections, including bacteraemia and other acute diseases in adults and immunocompromised individuals. We developed a novel system to study GBS within human monocytes to define the co-transcriptome of intracellular GBS (iGBS) and host cells simultaneously using dual RNA-sequencing (RNA-seq) to better define how this pathogen responds to host cells. Using human U937 monocytes and genome-sequenced GBS reference strain 874,391 in antibiotic protection assays we validated a system for dual-RNA seq based on measures of GBS and monocyte viability to ensure that the bacterial and host cell co-transcriptome reflected mainly intracellular (iGBS) rather than extracellular GBS. Elucidation of the co-transcriptome revealed 1119 dysregulated transcripts in iGBS with most genes, including several that encode virulence factors (e.g., scpB, hvgA, ribD, pil2b) exhibiting activation by upregulated expression. Infection with iGBS resulted in significant remodelling of the monocyte transcriptome, with 7587 transcripts differentially expressed including 7040 up-regulated and 547 down-regulated. qPCR confirmed that the most strongly activated genes included sht, encoding Streptococcal Histidine Triad Protein. An isogenic GBS mutant strain deficient in sht revealed a significant effect of this gene on phagocytosis of GBS and survival of the bacteria during systemic infection in mice. Identification of a novel contribution of sht to GBS virulence shows the co-transcriptome responses elucidated in GBS-infected monocytes help to shape the host-pathogen interaction and establish a role for sht in the response of the bacteria to phagocytic uptake. This study provides comprehension of concurrent transcriptional responses that occur in GBS and human monocytes that shape the host-pathogen interaction.
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10
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Bouabid C, Rabhi S, Thedinga K, Barel G, Tnani H, Rabhi I, Benkahla A, Herwig R, Guizani-Tabbane L. Host M-CSF induced gene expression drives changes in susceptible and resistant mice-derived BMdMs upon Leishmania major infection. Front Immunol 2023; 14:1111072. [PMID: 37187743 PMCID: PMC10175952 DOI: 10.3389/fimmu.2023.1111072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Leishmaniases are a group of diseases with different clinical manifestations. Macrophage-Leishmania interactions are central to the course of the infection. The outcome of the disease depends not only on the pathogenicity and virulence of the parasite, but also on the activation state, the genetic background, and the underlying complex interaction networks operative in the host macrophages. Mouse models, with mice strains having contrasting behavior in response to parasite infection, have been very helpful in exploring the mechanisms underlying differences in disease progression. We here analyzed previously generated dynamic transcriptome data obtained from Leishmania major (L. major) infected bone marrow derived macrophages (BMdMs) from resistant and susceptible mouse. We first identified differentially expressed genes (DEGs) between the M-CSF differentiated macrophages derived from the two hosts, and found a differential basal transcriptome profile independent of Leishmania infection. These host signatures, in which 75% of the genes are directly or indirectly related to the immune system, may account for the differences in the immune response to infection between the two strains. To gain further insights into the underlying biological processes induced by L. major infection driven by the M-CSF DEGs, we mapped the time-resolved expression profiles onto a large protein-protein interaction (PPI) network and performed network propagation to identify modules of interacting proteins that agglomerate infection response signals for each strain. This analysis revealed profound differences in the resulting responses networks related to immune signaling and metabolism that were validated by qRT-PCR time series experiments leading to plausible and provable hypotheses for the differences in disease pathophysiology. In summary, we demonstrate that the host's gene expression background determines to a large degree its response to L. major infection, and that the gene expression analysis combined with network propagation is an effective approach to help identifying dynamically altered mouse strain-specific networks that hold mechanistic information about these contrasting responses to infection.
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Affiliation(s)
- Cyrine Bouabid
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (PMBB), Institut Pasteur de Tunis, Tunis, Tunisia
- Faculty of Sciences of Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Sameh Rabhi
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (PMBB), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Kristina Thedinga
- Department Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gal Barel
- Department Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hedia Tnani
- Laboratory de BioInformatic, BioMathematic and BioStatistic (BIMS), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Imen Rabhi
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (PMBB), Institut Pasteur de Tunis, Tunis, Tunisia
- Higher Institute of Biotechnology at Sidi-Thabet (ISBST), Biotechnopole Sidi-Thabet- University of Manouba, Sidi-Thabet, Tunisia
| | - Alia Benkahla
- Laboratory de BioInformatic, BioMathematic and BioStatistic (BIMS), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Ralf Herwig
- Department Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lamia Guizani-Tabbane
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (PMBB), Institut Pasteur de Tunis, Tunis, Tunisia
- *Correspondence: Lamia Guizani-Tabbane,
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11
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Nemati Haravani T, Parvizi P, Hejazi SH, Sedaghat MM, Eskandarian A, Nateghi Rostami M. Evaluation of expression variations in virulence-related genes of Leishmania major after several culture passages compared with Phlebotomus papatasi isolated promastigotes. PLoS One 2023; 18:e0284240. [PMID: 37053214 PMCID: PMC10101501 DOI: 10.1371/journal.pone.0284240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
Cutaneous leishmaniasis (CL) is a prevalent infectious disease with considerable morbidity annually. Here, we aimed to investigate the likely variations in gene expression of glycoprotein63 (gp63), heat shock protein 70 (HSP70), histone, arginase, cysteine protease B (CPB), Leishmania homologue of receptors for activated C kinase (LACK), small hydrophilic endoplasmic reticulum-associated protein (SHERP) in metacyclic promastigotes of L. major isolated from Phlebotomus papatasi sand flies and promastigotes excessively cultured in culture medium. The parasites were collected from suspected CL cases in Pasteur Institute of Iran, cultured and inoculated into the female BALB/c mice (2×106 promastigotes). Sand flies were trapped in Qom province, fed with the blood of euthanized infected mice and subsequently dissected in order to isolate the midgut including stomodeal valve. The metacyclic promastigotes were isolated from Ph. papatasi (Pro-Ppap) using peanut agglutinin test (PNA), then continuously cultured in RPMI-1640 medium enriched with fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 mg/ml) to reach stationary phase (Pro-Stat). The gene expression was evaluated in both parasitic stages (Pro-Ppap and Pro-Stat) using qRT-PCR. Out results showed a significant increased gene expression at Pro-Ppap stage for gp63 (P = 0.002), SHERP (P = 0.001) and histone (P = 0.026) genes, in comparison with Pro-Stat stage. Noticeably, significant changes were, also, demonstrated in 10th to 15th passages [gp63 (P = 0.041), arginase (P = 0.016), LACK (P = 0.025)] and in 5th to 20th passage (SHERP) (P = 0.029). In conclusion, the findings of the present study seem to be essential in designing Leishmania studies, in particular regarding host-parasite interaction, immunization and infectivity studies.
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Affiliation(s)
- Taher Nemati Haravani
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Parviz Parvizi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Hossein Hejazi
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Mehdi Sedaghat
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbasali Eskandarian
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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12
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Jim KK, Aprianto R, Koning R, Domenech A, Kurushima J, van de Beek D, Vandenbroucke-Grauls CMJE, Bitter W, Veening JW. Pneumolysin promotes host cell necroptosis and bacterial competence during pneumococcal meningitis as shown by whole-animal dual RNA-seq. Cell Rep 2022; 41:111851. [PMID: 36543127 PMCID: PMC9794515 DOI: 10.1016/j.celrep.2022.111851] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/16/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Pneumolysin is a major virulence factor of Streptococcus pneumoniae that plays a key role in interaction with the host during invasive disease. How pneumolysin influences these dynamics between host and pathogen interaction during early phase of central nervous system infection in pneumococcal meningitis remains unclear. Using a whole-animal in vivo dual RNA sequencing (RNA-seq) approach, we identify pneumolysin-specific transcriptional responses in both S. pneumoniae and zebrafish (Danio rerio) during early pneumococcal meningitis. By functional enrichment analysis, we identify host pathways known to be activated by pneumolysin and discover the importance of necroptosis for host survival. Inhibition of this pathway using the drug GSK'872 increases host mortality during pneumococcal meningitis. On the pathogen's side, we show that pneumolysin-dependent competence activation is crucial for intra-host replication and virulence. Altogether, this study provides new insights into pneumolysin-specific transcriptional responses and identifies key pathways involved in pneumococcal meningitis.
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Affiliation(s)
- Kin Ki Jim
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Medical Microbiology and Infection Prevention, De Boelelaan 1117, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Neurology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Rieza Aprianto
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Rutger Koning
- Amsterdam UMC Location University of Amsterdam, Department of Neurology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Arnau Domenech
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Jun Kurushima
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Diederik van de Beek
- Amsterdam UMC Location University of Amsterdam, Department of Neurology, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Christina M J E Vandenbroucke-Grauls
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Medical Microbiology and Infection Prevention, De Boelelaan 1117, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Wilbert Bitter
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Medical Microbiology and Infection Prevention, De Boelelaan 1117, Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands; Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, 1081 Amsterdam, the Netherlands
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland.
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13
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Transcriptome Analysis of Intracellular Amastigotes of Clinical Leishmania infantum Lines from Therapeutic Failure Patients after Infection of Human Macrophages. Microorganisms 2022; 10:microorganisms10071304. [PMID: 35889023 PMCID: PMC9324091 DOI: 10.3390/microorganisms10071304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is considered to be one of the most neglected tropical diseases affecting humans and animals around the world. Due to the absence of an effective vaccine, current treatment is based on chemotherapy. However, the continuous appearance of drug resistance and therapeutic failure (TF) lead to an early obsolescence of treatments. Identification of the factors that contribute to TF and drug resistance in leishmaniasis will constitute a useful tool for establishing future strategies to control this disease. In this manuscript, we evaluated the transcriptomic changes in the intracellular amastigotes of the Leishmania infantum parasites isolated from patients with leishmaniasis and TF at 96 h post-infection of THP-1 cells. The adaptation of the parasites to their new environment leads to expression alterations in the genes involved mainly in the transport through cell membranes, energy and redox metabolism, and detoxification. Specifically, the gene that codes for the prostaglandin f2α synthase seems to be relevant in the pathogenicity and TF since it appears substantially upregulated in all the L. infantum lines. Overall, our results show that at the late infection timepoint, the transcriptome of the parasites undergoes significant changes that probably improve the survival of the Leishmania lines in the host cells, contributing to the TF phenotype as well as drug therapy evasion.
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14
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Chaparro V, Graber TE, Alain T, Jaramillo M. Transcriptional profiling of macrophages reveals distinct parasite stage-driven signatures during early infection by Leishmania donovani. Sci Rep 2022; 12:6369. [PMID: 35430587 PMCID: PMC9013368 DOI: 10.1038/s41598-022-10317-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 04/05/2022] [Indexed: 12/22/2022] Open
Abstract
Macrophages undergo swift changes in mRNA abundance upon pathogen invasion. Herein we describe early remodelling of the macrophage transcriptome during infection by amastigotes or promastigotes of Leishmania donovani. Approximately 10–16% of host mRNAs were differentially modulated in L. donovani-infected macrophages when compared to uninfected controls. This response was partially stage-specific as a third of changes in mRNA abundance were either exclusively driven by one of the parasite forms or significantly different between them. Gene ontology analyses identified categories associated with immune functions (e.g. antigen presentation and leukocyte activation) among significantly downregulated mRNAs during amastigote infection while cytoprotective-related categories (e.g. DNA repair and apoptosis inhibition) were enriched in upregulated transcripts. Interestingly a combination of upregulated (e.g. cellular response to IFNβ) and repressed (e.g. leukocyte activation, chemotaxis) immune-related transcripts were overrepresented in the promastigote-infected dataset. In addition, Ingenuity Pathway Analysis (IPA) associated specific mRNA subsets with a number of upstream transcriptional regulators predicted to be modulated in macrophages infected with L. donovani amastigotes (e.g. STAT1 inhibition) or promastigotes (e.g. NRF2, IRF3, and IRF7 activation). Overall, our results indicate that early parasite stage-driven transcriptional remodelling in macrophages contributes to orchestrate both protective and deleterious host cell responses during L. donovani infection.
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15
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Perea-Martínez A, García-Hernández R, Manzano JI, Gamarro F. Transcriptomic Analysis in Human Macrophages Infected with Therapeutic Failure Clinical Isolates of Leishmania infantum. ACS Infect Dis 2022; 8:800-810. [PMID: 35352952 PMCID: PMC9003231 DOI: 10.1021/acsinfecdis.1c00513] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Leishmaniasis is one of the neglected tropical diseases with a worldwide distribution, affecting humans and animals. In the absence of an effective vaccine, current treatment is through the use of chemotherapy; however, existing treatments have frequent appearance of drug resistance and therapeutic failure (TF). The identification of factors that contribute to TF in leishmaniasis will provide the basis for a future therapeutic strategy more efficient for the control of this disease. In this article, we have evaluated the transcriptomic changes in the host cells THP-1 after infection with clinical Leishmania infantum isolates from leishmaniasis patients with TF. Our results show that distinct L. infantum isolates differentially modulate host cell response, inducing phenotypic changes that probably may account for parasite survival and TF of patients. Analysis of differential expression genes (DEGs), with a statistical significance threshold of a fold change ≥ 2 and a false discovery rate value ≤ 0.05, revealed a different number of DEGs according to the Leishmanialine. Globally, there was a similar number of genes up- and downregulated in all the infected host THP-1 cells, with exception of Hi-L2221, which showed a higher number of downregulated DEGs. We observed a total of 58 DEGs commonly modulated in all infected host cells, including upregulated (log2FC ≥ 1) and downregulated (log2FC ≤ -1) genes. Based on the results obtained from the analysis of RNA-seq, volcano plot, and GO enrichment analysis, we identified the most significant transcripts of relevance for their possible contribution to the TF observed in patients with leishmaniasis.
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Affiliation(s)
- Ana Perea-Martínez
- Instituto de Parasitología y Biomedicina “López-Neyra”, IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Raquel García-Hernández
- Instituto de Parasitología y Biomedicina “López-Neyra”, IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - José Ignacio Manzano
- Instituto de Parasitología y Biomedicina “López-Neyra”, IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Francisco Gamarro
- Instituto de Parasitología y Biomedicina “López-Neyra”, IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda del Conocimiento 17, 18016 Armilla, Granada, Spain
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16
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García-Hernández R, Manzano JI, Perea-Martínez A, Gamarro F. New Insights on Drug-Resistant Clinical Isolates of Leishmania infantum-Infected Human Macrophages as Determined by Comparative Transcriptome Analyses. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:165-177. [PMID: 35172107 DOI: 10.1089/omi.2021.0185] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Leishmaniasis is the second most important neglected tropical parasitic disease after malaria. This disease is distributed worldwide and can be present in a variety of clinical forms, depending on the parasite species and host's genetic background. As chemotherapy is the only effective weapon whose effectiveness is limited by the frequent appearance of drug resistance and therapeutic failure, new therapeutic strategies are required. To better understand the factors that contribute to therapeutic failure and drug resistance in leishmaniasis, we studied the transcriptomic changes in host THP-1 cells after infection with clinical Leishmania infantum isolates with different susceptibilities to antileishmanial drugs by RNA-seq. Analysis of the differentially expressed genes (DEGs) in infected host cells revealed variations in DEG numbers in the THP-1-infected cells depending on the Leishmania line. A key conclusion of this study is that the modulation of host cells is Leishmania line dependent. Gene ontology enrichment analyses of DEGs indicated that certain biological processes were modulated in the infected host cells, specifically related to cellular metabolism, immune response, defense response, signaling pathways, and cell proliferation and apoptosis. Furthermore, this study provides new potential therapeutic markers and insights into the THP-1 host transcriptomic changes that occur after late infection with drug-resistant L. infantum clinical isolates.
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Affiliation(s)
| | - José Ignacio Manzano
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN-CSIC), Granada, Spain
| | - Ana Perea-Martínez
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN-CSIC), Granada, Spain
| | - Francisco Gamarro
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN-CSIC), Granada, Spain
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17
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Mas A, Martínez-Rodrigo A, Carrión J, Orden JA, Alzate JF, Domínguez-Bernal G, Horcajo P. Transcriptomic Profile of Canine DH82 Macrophages Infected by Leishmania infantum Promastigotes with Different Virulence Behavior. Int J Mol Sci 2022; 23:ijms23031466. [PMID: 35163386 PMCID: PMC8835757 DOI: 10.3390/ijms23031466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/17/2022] [Accepted: 01/25/2022] [Indexed: 02/07/2023] Open
Abstract
Zoonotic visceral leishmaniosis caused by Leishmania infantum is an endemic disease in the Mediterranean Basin affecting mainly humans and dogs, the main reservoir. The leishmaniosis outbreak declared in the Community of Madrid (Spain) led to a significant increase in human disease incidence without enhancing canine leishmaniosis prevalence, suggesting a better adaptation of the outbreak's isolates by other host species. One of the isolates obtained in the focus, IPER/ES/2012/BOS1FL1 (BOS1FL1), has previously demonstrated a different phenotype than the reference strain MCAN/ES/1996/BCN150 (BCN150), characterized by a lower infectivity when interacting with canine macrophages. Nevertheless, not enough changes in the cell defensive response were found to support their different behavior. Thus, we decided to investigate the molecular mechanisms involved in the interaction of both parasites with DH82 canine macrophages by studying their transcriptomic profiles developed after infection using RNA sequencing. The results showed a common regulation induced by both parasites in the phosphoinositide-3-kinase-protein kinase B/Akt and NOD-like receptor signaling pathways. However, other pathways, such as phagocytosis and signal transduction, including tumor necrosis factor, mitogen-activated kinases and nuclear factor-κB, were only regulated after infection with BOS1FL1. These differences could contribute to the reduced infection ability of the outbreak isolates in canine cells. Our results open a new avenue to investigate the true role of adaptation of L. infantum isolates in their interaction with their different hosts.
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Affiliation(s)
- Alicia Mas
- INMIVET, Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain; (A.M.); (A.M.-R.); (J.C.); (J.A.O.)
| | - Abel Martínez-Rodrigo
- INMIVET, Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain; (A.M.); (A.M.-R.); (J.C.); (J.A.O.)
| | - Javier Carrión
- INMIVET, Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain; (A.M.); (A.M.-R.); (J.C.); (J.A.O.)
| | - José Antonio Orden
- INMIVET, Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain; (A.M.); (A.M.-R.); (J.C.); (J.A.O.)
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Departamento de Microbiología y Parasitología, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Gustavo Domínguez-Bernal
- INMIVET, Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain; (A.M.); (A.M.-R.); (J.C.); (J.A.O.)
- Correspondence: ; Tel.: +34-913943814
| | - Pilar Horcajo
- Animal Health and Zoonoses (SALUVET) Group, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, 28040 Madrid, Spain;
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18
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Smirlis D, Dingli F, Sabatet V, Roth A, Knippschild U, Loew D, Späth GF, Rachidi N. Identification of the Host Substratome of Leishmania-Secreted Casein Kinase 1 Using a SILAC-Based Quantitative Mass Spectrometry Assay. Front Cell Dev Biol 2022; 9:800098. [PMID: 35047509 PMCID: PMC8762337 DOI: 10.3389/fcell.2021.800098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/13/2021] [Indexed: 12/27/2022] Open
Abstract
Leishmaniasis is a severe public health problem, caused by the protozoan Leishmania. This parasite has two developmental forms, extracellular promastigote in the insect vector and intracellular amastigote in the mammalian host where it resides inside the phagolysosome of macrophages. Little is known about the virulence factors that regulate host-pathogen interactions and particularly host signalling subversion. All the proteomes of Leishmania extracellular vesicles identified the presence of Leishmania casein kinase 1 (L-CK1.2), a signalling kinase. L-CK1.2 is essential for parasite survival and thus might be essential for host subversion. To get insights into the functions of L-CK1.2 in the macrophage, the systematic identification of its host substrates is crucial, we thus developed an easy method to identify substrates, combining phosphatase treatment, in vitro kinase assay and Stable Isotope Labelling with Amino acids in Cell (SILAC) culture-based mass spectrometry. Implementing this approach, we identified 225 host substrates as well as a potential novel phosphorylation motif for CK1. We confirmed experimentally the enrichment of our substratome in bona fide L-CK1.2 substrates and showed they were also phosphorylated by human CK1δ. L-CK1.2 substratome is enriched in biological processes such as "viral and symbiotic interaction," "actin cytoskeleton organisation" and "apoptosis," which are consistent with the host pathways modified by Leishmania upon infection, suggesting that L-CK1.2 might be the missing link. Overall, our results generate important mechanistic insights into the signalling of host subversion by these parasites and other microbial pathogens adapted for intracellular survival.
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Affiliation(s)
- Despina Smirlis
- Institut Pasteur, Université de Paris, Institut National de Santé et Recherche Médicale INSERM U1201, Unité de parasitologie Moléculaire et Signalisation, Paris, France.,Hellenic Pasteur Institute, Athens, Greece
| | - Florent Dingli
- Laboratoire de Spectrométrie de Masse Protéomique (LSMP), Centre de Recherche, Institut Curie, PSL Research University, Paris, France
| | - Valentin Sabatet
- Laboratoire de Spectrométrie de Masse Protéomique (LSMP), Centre de Recherche, Institut Curie, PSL Research University, Paris, France
| | - Aileen Roth
- Department of General and Visceral Surgery, Centre of Surgery, University Hospital Ulm, Ulm, Germany
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Centre of Surgery, University Hospital Ulm, Ulm, Germany
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique (LSMP), Centre de Recherche, Institut Curie, PSL Research University, Paris, France
| | - Gerald F Späth
- Institut Pasteur, Université de Paris, Institut National de Santé et Recherche Médicale INSERM U1201, Unité de parasitologie Moléculaire et Signalisation, Paris, France
| | - Najma Rachidi
- Institut Pasteur, Université de Paris, Institut National de Santé et Recherche Médicale INSERM U1201, Unité de parasitologie Moléculaire et Signalisation, Paris, France
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19
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Salloum T, Tokajian S, Hirt RP. Advances in Understanding Leishmania Pathobiology: What Does RNA-Seq Tell Us? Front Cell Dev Biol 2021; 9:702240. [PMID: 34540827 PMCID: PMC8440825 DOI: 10.3389/fcell.2021.702240] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/30/2021] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is a vector-borne disease caused by a protozoa parasite from over 20 Leishmania species. The clinical manifestations and the outcome of the disease vary greatly. Global RNA sequencing (RNA-Seq) analyses emerged as a powerful technique to profile the changes in the transcriptome that occur in the Leishmania parasites and their infected host cells as the parasites progresses through their life cycle. Following the bite of a sandfly vector, Leishmania are transmitted to a mammalian host where neutrophils and macrophages are key cells mediating the interactions with the parasites and result in either the elimination the infection or contributing to its proliferation. This review focuses on RNA-Seq based transcriptomics analyses and summarizes the main findings derived from this technology. In doing so, we will highlight caveats in our understanding of the parasite’s pathobiology and suggest novel directions for research, including integrating more recent data highlighting the role of the bacterial members of the sandfly gut microbiota and the mammalian host skin microbiota in their potential role in influencing the quantitative and qualitative aspects of leishmaniasis pathology.
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Affiliation(s)
- Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Robert P Hirt
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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20
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Sandholt AKS, Wattrang E, Lilja T, Ahola H, Lundén A, Troell K, Svärd SG, Söderlund R. Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens. BMC Genomics 2021; 22:660. [PMID: 34521339 PMCID: PMC8438895 DOI: 10.1186/s12864-021-07959-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/29/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Coccidiosis is an infectious disease with large negative impact on the poultry industry worldwide. It is an enteric infection caused by unicellular Apicomplexan parasites of the genus Eimeria. The present study aimed to gain more knowledge about interactions between parasites and the host immune system during the early asexual replication phase of E. tenella in chicken caeca. For this purpose, chickens were experimentally infected with E. tenella oocysts, sacrificed on days 1-4 and 10 after infection and mRNA from caecal tissues was extracted and sequenced. RESULTS Dual RNA-seq analysis revealed time-dependent changes in both host and parasite gene expression during the course of the infection. Chicken immune activation was detected from day 3 and onwards with the highest number of differentially expressed immune genes recorded on day 10. Among early (days 3-4) responses up-regulation of genes for matrix metalloproteinases, several chemokines, interferon (IFN)-γ along with IFN-stimulated genes GBP, IRF1 and RSAD2 were noted. Increased expression of genes with immune suppressive/regulatory effects, e.g. IL10, SOCS1, SOCS3, was also observed among early responses. For E. tenella a general up-regulation of genes involved in protein expression and energy metabolism as well as a general down-regulation genes for DNA and RNA processing were observed during the infection. Specific E. tenella genes with altered expression during the experiment include those for proteins in rhoptry and microneme organelles. CONCLUSIONS The present study provides novel information on both the transcriptional activity of E. tenella during schizogony in ceacal tissue and of the local host responses to parasite invasion during this phase of infection. Results indicate a role for IFN-γ and IFN-stimulated genes in the innate defence against Eimeria replication.
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Affiliation(s)
- Arnar K S Sandholt
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Eva Wattrang
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden.
| | - Tobias Lilja
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Harri Ahola
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Anna Lundén
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Karin Troell
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Robert Söderlund
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
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21
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Ackland J, Heinson AI, Cleary DW, Christodoulides M, Wilkinson TMA, Staples KJ. Dual RNASeq Reveals NTHi-Macrophage Transcriptomic Changes During Intracellular Persistence. Front Cell Infect Microbiol 2021; 11:723481. [PMID: 34497778 PMCID: PMC8419319 DOI: 10.3389/fcimb.2021.723481] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is a pathobiont which chronically colonises the airway of individuals with chronic respiratory disease and is associated with poor clinical outcomes. It is unclear how NTHi persists in the airway, however accumulating evidence suggests that NTHi can invade and persist within macrophages. To better understand the mechanisms of NTHi persistence within macrophages, we developed an in vitro model of NTHi intracellular persistence using human monocyte-derived macrophages (MDM). Dual RNA Sequencing was used to assess MDM and NTHi transcriptomic regulation occurring simultaneously during NTHi persistence. Analysis of the macrophage response to NTHi identified temporally regulated transcriptomic profiles, with a specific 'core' profile displaying conserved expression of genes across time points. Gene list enrichment analysis identified enrichment of immune responses in the core gene set, with KEGG pathway analysis revealing specific enrichment of intracellular immune response pathways. NTHi persistence was facilitated by modulation of bacterial metabolic, stress response and ribosome pathways. Levels of NTHi genes bioC, mepM and dps were differentially expressed by intracellular NTHi compared to planktonic NTHi, indicating that the transcriptomic adaption was distinct between the two different NTHi lifestyles. Overall, this study provides crucial insights into the transcriptomic adaptations facilitating NTHi persistence within macrophages. Targeting these reported pathways with novel therapeutics to reduce NTHi burden in the airway could be an effective treatment strategy given the current antimicrobial resistance crisis and lack of NTHi vaccines.
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Affiliation(s)
- Jodie Ackland
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ashley I Heinson
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - David W Cleary
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Myron Christodoulides
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Tom M A Wilkinson
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom.,Wessex Investigational Sciences Hub, Southampton General Hospital, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Karl J Staples
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom.,Wessex Investigational Sciences Hub, Southampton General Hospital, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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22
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Gomez MA, Belew AT, Navas A, Rosales-Chilama M, Murillo J, Dillon LAL, Alexander TA, Martinez-Valencia A, El-Sayed NM. Early Leukocyte Responses in Ex-Vivo Models of Healing and Non-Healing Human Leishmania (Viannia) panamensis Infections. Front Cell Infect Microbiol 2021; 11:687607. [PMID: 34557423 PMCID: PMC8453012 DOI: 10.3389/fcimb.2021.687607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/16/2021] [Indexed: 11/21/2022] Open
Abstract
Early host-pathogen interactions drive the host response and shape the outcome of natural infections caused by intracellular microorganisms. These interactions involve a number of immune and non-immune cells and tissues, along with an assortment of host and pathogen-derived molecules. Our current knowledge has been predominantly derived from research on the relationships between the pathogens and the invaded host cell(s), limiting our understanding of how microbes elicit and modulate immunological responses at the organismal level. In this study, we explored the early host determinants of healing and non-healing responses in human cutaneous leishmaniasis (CL) caused by Leishmania (Viannia) panamensis. We performed a comparative transcriptomic profiling of peripheral blood mononuclear cells from healthy donors (PBMCs, n=3) exposed to promastigotes isolated from patients with chronic (CHR, n=3) or self-healing (SH, n=3) CL, and compared these to human macrophage responses. Transcriptomes of L. V. panamensis-infected PBMCs showed enrichment of functional gene categories derived from innate as well as adaptive immune cells signatures, demonstrating that Leishmania modulates adaptive immune cell functions as early as after 24h post interaction with PBMCs from previously unexposed healthy individuals. Among differentially expressed PBMC genes, four broad categories were commonly modulated by SH and CHR strains: cell cycle/proliferation/differentiation, metabolism of macromolecules, immune signaling and vesicle trafficking/transport; the first two were predominantly downregulated, and the latter upregulated in SH and CHR as compared to uninfected samples. Type I IFN signaling genes were uniquely up-regulated in PBMCs infected with CHR strains, while genes involved in the immunological synapse were uniquely downregulated in SH infections. Similarly, pro-inflammatory response genes were upregulated in isolated macrophages infected with CHR strains. Our data demonstrate that early responses during Leishmania infection extend beyond innate cell and/or phagocytic host cell functions, opening new frontiers in our understanding of the triggers and drivers of human CL.
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Affiliation(s)
- Maria Adelaida Gomez
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Universidad IcesiI, Cali, Colombia
| | - Ashton Trey Belew
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, United States
| | - Adriana Navas
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
| | - Mariana Rosales-Chilama
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Universidad IcesiI, Cali, Colombia
| | - Julieth Murillo
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Pontificia Universidad Javeriana, Cali, Colombia
| | - Laura A. L. Dillon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, United States
| | - Theresa A. Alexander
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | | | - Najib M. El-Sayed
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, United States
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23
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Palacios G, Diaz-Solano R, Valladares B, Dorta-Guerra R, Carmelo E. Early Transcriptional Liver Signatures in Experimental Visceral Leishmaniasis. Int J Mol Sci 2021; 22:7161. [PMID: 34281214 PMCID: PMC8267970 DOI: 10.3390/ijms22137161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 01/01/2023] Open
Abstract
Transcriptional analysis of complex biological scenarios has been used extensively, even though sometimes the results of such analysis may prove imprecise or difficult to interpret due to an overwhelming amount of information. In this study, a large-scale real-time qPCR experiment was coupled to multivariate statistical analysis in order to describe the main immunological events underlying the early L. infantum infection in livers of BALB/c mice. High-throughput qPCR was used to evaluate the expression of 223 genes related to immunological response and metabolism 1, 3, 5, and 10 days post infection. This integrative analysis showed strikingly different gene signatures at 1 and 10 days post infection, revealing the progression of infection in the experimental model based on the upregulation of particular immunological response patterns and mediators. The gene signature 1 day post infection was not only characterized by the upregulation of mediators involved in interferon signaling and cell chemotaxis, but also the upregulation of some inhibitory markers. In contrast, at 10 days post infection, the upregulation of many inflammatory and Th1 markers characterized a more defined gene signature with the upregulation of mediators in the IL-12 signaling pathway. Our results reveal a significant connection between the expression of innate immune response and metabolic and inhibitory markers in early L. infantum infection of the liver.
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Affiliation(s)
- Génesis Palacios
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de la Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n, 38200 La Laguna (Tenerife), Spain; (G.P.); (R.D.-S.); (B.V.); (R.D.-G.)
| | - Raquel Diaz-Solano
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de la Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n, 38200 La Laguna (Tenerife), Spain; (G.P.); (R.D.-S.); (B.V.); (R.D.-G.)
| | - Basilio Valladares
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de la Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n, 38200 La Laguna (Tenerife), Spain; (G.P.); (R.D.-S.); (B.V.); (R.D.-G.)
- Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38200 La Laguna (Tenerife), Spain
- Red de Investigación Colaborativa en Enfermedades Tropicales (RICET)
| | - Roberto Dorta-Guerra
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de la Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n, 38200 La Laguna (Tenerife), Spain; (G.P.); (R.D.-S.); (B.V.); (R.D.-G.)
- Departamento de Matemáticas, Estadística e Investigación Operativa, Facultad de Ciencias, Universidad de La Laguna, 38200 La Laguna (Tenerife), Spain
| | - Emma Carmelo
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de la Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n, 38200 La Laguna (Tenerife), Spain; (G.P.); (R.D.-S.); (B.V.); (R.D.-G.)
- Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38200 La Laguna (Tenerife), Spain
- Departamento de Matemáticas, Estadística e Investigación Operativa, Facultad de Ciencias, Universidad de La Laguna, 38200 La Laguna (Tenerife), Spain
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24
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Park YS, Park JS, Lee S, Jung SH, Kim SK, Ryu CM. Simultaneous profiling of Arabidopsis thaliana and Vibrio vulnificus MO6-24/O transcriptomes by dual RNA-seq analysis. Comput Struct Biotechnol J 2021; 19:2084-2096. [PMID: 33995904 PMCID: PMC8085779 DOI: 10.1016/j.csbj.2021.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 01/16/2023] Open
Abstract
We previously demonstrated that a marine bacterial pathogen Vibrio vulnificus isolated from sea foods modulated gene expression levels and defense responses of a land plant Arabidopsis thaliana. Although the interaction between V. vulnificus and A. thaliana was verified under artificial and greenhouse conditions, the simultaneous changes in host and pathogen transcriptomes remained obscure. In this study, we simultaneously analyzed the transcriptome of V. vulnificus MO6-24/O and A. thaliana by dual RNA-sequencing analysis. Disease symptoms appeared at 5 and 7 days post-inoculation in vitro and post-infiltration in planta, respectively. A total of 31, 128, 303, 219, and 130 differentially expressed genes (DEGs) were identified in V. vulnificus MO6-24/O at 3, 6, 12, 24, and 48 h post-infiltration. Out of these, 14 genes involved in the virulence and pathogenicity of V. vulnificus MO6 were characterized. These genes were clustered into six categories, including adherence, antiphagocytosis, chemotaxis and motility, iron uptake, toxin and secretion system. In plant side, the bacterium DEGs potentially played a pivotal role in activating pattern recognition receptors (PRRs)-mediated defense responses. A. thaliana genes related to PRRs, reactive oxygen species burst, mitogen-activated protein kinase cascade induction, salicylic acid, jasmonic acid, ethylene, abscisic acid, auxin, gibberellin, and cytokinin were highly induced by V. vulnificus MO6-24/O challenge. Taken together, our results indicate that the sophisticated communication between a marine bacterial pathogen V. vulnificus and A. thaliana occurs. It is the first report demonstration that V. vulnificus actively modulates its virulence factors and potential host immune regulator in a land plant species.
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Affiliation(s)
- Yong-Soon Park
- Biotechnology Research Institute, College of Natural Sciences, Chungbuk National University, Cheongju 28644, South Korea
| | - Jong-Seok Park
- Department of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju 28644, South Korea
| | - Soohyun Lee
- Molecular Phytobacteriology Laboratory, Infection Disease Research Center, KRIBB, Daejeon 34141, South Korea
| | - Sung-Hee Jung
- Molecular Phytobacteriology Laboratory, Infection Disease Research Center, KRIBB, Daejeon 34141, South Korea
| | - Seon-Kyu Kim
- Personalized Medical Genomics Research Center, KRIBB, Daejeon 34141, South Korea
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, Infection Disease Research Center, KRIBB, Daejeon 34141, South Korea.,Biosystem and Bioengineering Program, University of Science and Technology (UST) KRIBB School, Daejeon 34141, South Korea
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25
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Parab AR, McCall LI. Tryp-ing Up Metabolism: Role of Metabolic Adaptations in Kinetoplastid Disease Pathogenesis. Infect Immun 2021; 89:e00644-20. [PMID: 33526564 PMCID: PMC8090971 DOI: 10.1128/iai.00644-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Today, more than a billion people-one-sixth of the world's population-are suffering from neglected tropical diseases. Human African trypanosomiasis, Chagas disease, and leishmaniasis are neglected tropical diseases caused by protozoan parasites belonging to the genera Trypanosoma and Leishmania About half a million people living in tropical and subtropical regions of the world are at risk of contracting one of these three infections. Kinetoplastids have complex life cycles with different morphologies and unique physiological requirements at each life cycle stage. This review covers the latest findings on metabolic pathways impacting disease pathogenesis of kinetoplastids within the mammalian host. Nutrient availability is a key factor shaping in vivo parasite metabolism; thus, kinetoplastids display significant metabolic flexibility. Proteomic and transcriptomic profiles show that intracellular trypanosomatids are able to switch to an energy-efficient metabolism within the mammalian host system. Host metabolic changes can also favor parasite persistence, and contribute to symptom development, in a location-specific fashion. Ultimately, targeted and untargeted metabolomics studies have been a valuable approach to elucidate the specific biochemical pathways affected by infection within the host, leading to translational drug development and diagnostic insights.
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Affiliation(s)
- Adwaita R Parab
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Laura-Isobel McCall
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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26
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Hu X, Liu X, Li C, Zhang Y, Li C, Li Y, Chen Y, Guo H, Bai X, Liu M. Time-resolved transcriptional profiling of Trichinella-infected murine myocytes helps to elucidate host-pathogen interactions in the muscle stage. Parasit Vectors 2021; 14:130. [PMID: 33648561 PMCID: PMC7919990 DOI: 10.1186/s13071-021-04624-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/03/2021] [Indexed: 11/30/2022] Open
Abstract
Background Parasites of the genus Trichinella are the pathogenic agents of trichinellosis, which is a widespread and severe foodborne parasitic disease. Trichinella spiralis resides primarily in mammalian skeletal muscle cells. After invading the cells of the host organism, T. spiralis must elude or invalidate the host’s innate and adaptive immune responses to survive. It is necessary to characterize the pathogenesis of trichinellosis to help to prevent the occurrence and further progression of this disease. The aims of this study were to elucidate the mechanisms of nurse cell formation, pathogenesis and immune evasion of T. spiralis, to provide valuable information for further research investigating the basic cell biology of Trichinella-infected muscle cells and the interaction between T. spiralis and its host. Methods We performed transcriptome profiling by RNA sequencing to identify global changes at 1, 3, 7, 10 and 15 days post-infection (dpi) in gene expression in the diaphragm after the parasite entered and persisted within the murine myocytes; the mice were infected by intravenous injection of newborn larvae. Gene expression analysis was based on the alignment results. Differentially expressed genes (DEGs) were identified based on their expression levels in various samples, and functional annotation and enrichment analysis were performed. Results The most extensive and dynamic gene expression responses in host diaphragms were observed during early infection (1 dpi). The number of DEGs and genes annotated in the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases decreased significantly in the infected mice compared to the uninfected mice at 3 and 7 dpi, suddenly increased sharply at 10 dpi, and then decreased to a lower level at 15 dpi, similar to that observed at 3 and 7 dpi. The massive initial reaction of the murine muscle cells to Trichinella infection steadied in the later stages of infection, with little additional changes detected for the remaining duration of the studied process. Although there were hundreds of DEGs at each time point, only 11 genes were consistently up- or downregulated at all 5 time points. Conclusions The gene expression patterns identified in this study can be employed to characterize the coordinated response of T. spiralis-infected myocytes in a time-resolved manner. This comprehensive dataset presents a distinct and sensitive picture of the interaction between host and parasite during intracellular infection, which can help to elucidate how pathogens evade host defenses and coordinate the biological functions of host cells to survive in the mammalian environment. ![]()
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Affiliation(s)
- Xiaoxiang Hu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Xiaolei Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Chen Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yulu Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Chengyao Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yanfeng Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yingxi Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Heng Guo
- Beijing Hi-Tech Institute, Beijing, 100085, China
| | - Xue Bai
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| | - Mingyuan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China.
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27
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Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella. Parasitology 2021; 148:712-725. [PMID: 33536090 PMCID: PMC8056837 DOI: 10.1017/s0031182021000111] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The study aimed to monitor parasite and host gene expression during the early stages of Eimeria tenella infection of chicken cells using dual RNA-Seq analysis. For this, we used chicken macrophage-like cell line HD11 cultures infected in vitro with purified E. tenella sporozoites. Cultures were harvested between 2 and 72 h post-infection and mRNA was extracted and sequenced. Dual RNA-Seq analysis showed clear patterns of altered expression for both parasite and host genes during infection. For example, genes in the chicken immune system showed upregulation early (2–4 h), a strong downregulation of genes across the immune system at 24 h and a repetition of early patterns at 72 h, indicating that invasion by a second generation of parasites was occurring. The observed downregulation may be due to immune self-regulation or to immune evasive mechanisms exerted by E. tenella. Results also suggested pathogen recognition receptors involved in E. tenella innate recognition, MRC2, TLR15 and NLRC5 and showed distinct chemokine and cytokine induction patterns. Moreover, the expression of several functional categories of Eimeria genes, such as rhoptry kinase genes and microneme genes, were also examined, showing distinctive differences which were expressed in sporozoites and merozoites.
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28
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Restrepo CM, Llanes A, Herrera L, Ellis E, Lleonart R, Fernández PL. Gene expression patterns associated with Leishmania panamensis infection in macrophages from BALB/c and C57BL/6 mice. PLoS Negl Trop Dis 2021; 15:e0009225. [PMID: 33617537 PMCID: PMC7932533 DOI: 10.1371/journal.pntd.0009225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/04/2021] [Accepted: 02/09/2021] [Indexed: 01/22/2023] Open
Abstract
Leishmania parasites can trigger different host immune responses that result in varying levels of disease severity. The C57BL/6 and BALB/c mouse strains are among the host models commonly used for characterizing the immunopathogenesis of Leishmania species and the possible antileishmanial effect of novel drug candidates. C57BL/6 mice tend to be resistant to Leishmania infections, whereas BALB/c mice display a susceptible phenotype. Studying species-specific interactions between Leishmania parasites and different host systems is a key step to characterize and validate these models for in vivo studies. Here, we use RNA-Seq and differential expression analysis to characterize the transcriptomic profiles of C57BL/6 and BALB/c peritoneal-derived macrophages in response to Leishmania panamensis infection. We observed differences between BALB/c and C57BL/6 macrophages regarding pathways associated with lysosomal degradation, arginine metabolism and the regulation of cell cycle. We also observed differences in the expression of chemokine and cytokine genes associated with regulation of immune responses. In conclusion, infection with L. panamensis induced an inflammatory gene expression pattern in C57BL/6 macrophages that is more consistently associated with a classic macrophage M1 activation, whereas in BALB/c macrophages a gene expression pattern consistent with an intermediate inflammatory response was observed.
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Affiliation(s)
- Carlos M. Restrepo
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Republic of Panama
| | - Alejandro Llanes
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Republic of Panama
| | - Lizzi Herrera
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Republic of Panama
| | - Esteban Ellis
- Departamento de Biotecnología, Facultad de Ciencias de la Salud, Universidad Latina de Panamá, Panama City, Panama, Republic of Panama
| | - Ricardo Lleonart
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Republic of Panama
| | - Patricia L. Fernández
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Republic of Panama
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Aoki JI, Muxel SM, Laranjeira-Silva MF, Zampieri RA, Müller KE, Nerland AH, Floeter-Winter LM. Dual transcriptome analysis reveals differential gene expression modulation influenced by Leishmania arginase and host genetic background. Microb Genom 2020; 6:mgen000427. [PMID: 32886592 PMCID: PMC7643972 DOI: 10.1099/mgen.0.000427] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/13/2020] [Indexed: 01/04/2023] Open
Abstract
The outcome of Leishmania infection is strongly influenced by the host's genetic background. BALB/c mice are susceptible to Leishmania infection, while C57BL/6 mice show discrete resistance. Central to the fate of the infection is the availability of l-arginine and the related metabolic processes in the host and parasite. Depending on l-arginine availability, nitric oxide synthase 2 (NOS2) of the host cell produces nitric oxide (NO) controlling the parasite growth. On the other hand, Leishmania can also use host l-arginine for the production of polyamines through its own arginase activity, thus favouring parasite replication. Considering RNA-seq data, we analysed the dual modulation of host and parasite gene expression of BALB/c or C57BL/6 mouse bone marrow-derived macrophages (BMDMs) after 4 h of infection with Leishmania amazonensis wild-type (La-WT) or L. amazonensis arginase knockout (La-arg-). We identified 12 641 host transcripts and 8282 parasite transcripts by alignment analysis with the respective Mus musculus and L. mexicana genomes. The comparison of BALB/c_La-arg-versus BALB/c_La-WT revealed 233 modulated transcripts, with most related to the immune response and some related to the amino acid transporters and l-arginine metabolism. In contrast, the comparison of C57BL/6_La-arg-vs. C57BL/6_La-WT revealed only 30 modulated transcripts, including some related to the immune response but none related to amino acid transport or l-arginine metabolism. The transcriptome profiles of the intracellular amastigote revealed 94 modulated transcripts in the comparison of La-arg-_BALB/c vs. La-WT_BALB/c and 45 modulated transcripts in the comparison of La-arg-_C57BL/6 vs. La-WT_C57BL/6. Taken together, our data present new insights into the impact of parasite arginase activity on the orchestration of the host gene expression modulation, including in the immune response and amino acid transport and metabolism, mainly in susceptible BALB/c-infected macrophages. Moreover, we show how parasite arginase activity affects parasite gene expression modulation, including amino acid uptake and amastin expression.
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Affiliation(s)
- Juliana Ide Aoki
- Department of Physiology, Institute of Bioscience, University of São Paulo, São Paulo, Brazil
| | - Sandra Marcia Muxel
- Department of Physiology, Institute of Bioscience, University of São Paulo, São Paulo, Brazil
| | | | | | - Karl Erik Müller
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Internal Medicine, Drammen Hospital, Drammen, Norway
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30
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Pessenda G, da Silva JS. Arginase and its mechanisms in Leishmania persistence. Parasite Immunol 2020; 42:e12722. [PMID: 32294247 DOI: 10.1111/pim.12722] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/14/2020] [Accepted: 04/07/2020] [Indexed: 12/12/2022]
Abstract
Leishmaniasis is a neglected infectious disease with clinical presentations ranging from asymptomatic or mild symptoms to chronic infection and eventual death. The mechanisms of disease susceptibility and pathology have been extensively studied, but there are no steadfast rules regarding leishmaniasis. A Th1 response is usually associated with infection control, while a predominant Th2 response is detrimental to the patient. In this scenario, the enzymes arginase and inducible nitric oxide synthase represent two possible pathways of immune response. While the former contributes to parasite replication, the latter is crucial for its control. In the present review, we collected study results that associate arginase expression in patients and in experimental models with disease susceptibility/chronicity and show some proposed mechanisms that explain the role of arginase in maintaining Leishmania infection, including polyamine and thiol synthesis, tissue-resident macrophage (TRM) proliferation and activation and T-cell suppression and exhaustion.
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Affiliation(s)
- Gabriela Pessenda
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - João Santana da Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Fundação Oswaldo Cruz Bi-institucional, Ribeirão Preto, Brazil
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31
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Ulusan Ö, Mert U, Sadıqova A, Öztürk S, Caner A. Identification of gene expression profiles in Leishmania major infection by integrated bioinformatics analyses. Acta Trop 2020; 208:105517. [PMID: 32360239 DOI: 10.1016/j.actatropica.2020.105517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 10/24/2022]
Abstract
Gene expression profiling in mouse models of leishmaniasis has given useful information to understand the molecular pathways active in lesions and to discover new diagnostic/therapeutic targets. Although the host response plays a critical role in protection from leishmaniasis and promoting disease severity, there are still unexplained aspects in the mechanism of non-healing cutaneous lesions, which need biomarkers for both targeted- therapy and diagnosis. To address this, transcriptional profiling of the skin lesions obtained from BALB/c mice infected with Leishmania major and healthy skin from naïve mice were evaluated by bioinformatics analysis, and then the results were validated by Revers Transcriptase-PCR. Five genes among the up-regulated differentially expressed genes named FCGR4, CCL4, CXCL9, Arg1 and IL-1β were found to have relatively high diagnostic value for CL due to L. major. Pathway analysis revealed that Triggering Receptor Expressed On Myeloid Cells 1 (TREM1) signaling pathways are active in cutaneous lesions, providing new insights for the understanding and treatment of leishmaniasis.
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Affiliation(s)
- Özlem Ulusan
- Department of Parasitology, Ege University Medical School, Izmir, Turkey
| | - Ufuk Mert
- Department of Basic Oncology, Ege University, Institute of Health Sciences, Izmir, Turkey
| | - Aygül Sadıqova
- Infectious Disease Division, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Sercan Öztürk
- Departments of Computer Science, Dokuz Eylül University, Izmir, Turkey
| | - Ayse Caner
- Department of Parasitology, Ege University Medical School, Izmir, Turkey; Department of Basic Oncology, Ege University, Institute of Health Sciences, Izmir, Turkey; Department of Bioinformatics, Ege University, Institute of Health Sciences, Izmir, Turkey; Departments of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Loaiza CD, Duhan N, Lister M, Kaundal R. In silico prediction of host-pathogen protein interactions in melioidosis pathogen Burkholderia pseudomallei and human reveals novel virulence factors and their targets. Brief Bioinform 2020; 22:5842243. [PMID: 32444871 DOI: 10.1093/bib/bbz162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 11/13/2019] [Accepted: 11/20/2019] [Indexed: 12/13/2022] Open
Abstract
The aerobic, Gram-negative motile bacillus, Burkholderia pseudomallei is a facultative intracellular bacterium causing melioidosis, a critical disease of public health importance, which is widely endemic in the tropics and subtropical regions of the world. Melioidosis is associated with high case fatality rates in animals and humans; even with treatment, its mortality is 20-50%. It also infects plants and is designated as a biothreat agent. B. pseudomallei is pathogenic due to its ability to invade, resist factors in serum and survive intracellularly. Despite its importance, to date only a few effector proteins have been functionally characterized, and there is not much information regarding the host-pathogen protein-protein interactions (PPI) of this system, which are important to studying infection mechanisms and thereby develop prevention measures. We explored two computational approaches, the homology-based interolog and the domain-based method, to predict genome-scale host-pathogen interactions (HPIs) between two different strains of B. pseudomallei (prototypical, and highly virulent) and human. In total, 76 335 common HPIs (between the two strains) were predicted involving 8264 human and 1753 B. pseudomallei proteins. Among the unique PPIs, 14 131 non-redundant HPIs were found to be unique between the prototypical strain and human, compared to 3043 non-redundant HPIs between the highly virulent strain and human. The protein hubs analysis showed that most B. pseudomallei proteins formed a hub with human dnaK complex proteins associated with tuberculosis, a disease similar in symptoms to melioidosis. In addition, drug-binding and carbohydrate-binding mechanisms were found overrepresented within the host-pathogen network, and metabolic pathways were frequently activated according to the pathway enrichment. Subcellular localization analysis showed that most of the pathogen proteins are targeting human proteins inside cytoplasm and nucleus. We also discovered the host targets of the drug-related pathogen proteins and proteins that form T3SS and T6SS in B. pseudomallei. Additionally, a comparison between the unique PPI patterns present in the prototypical and highly virulent strains was performed. The current study is the first report on developing a genome-scale host-pathogen protein interaction networks between the human and B. pseudomallei, a critical biothreat agent. We have identified novel virulence factors and their interacting partners in the human proteome. These PPIs can be further validated by high-throughput experiments and may give new insights on how B. pseudomallei interacts with its host, which will help medical researchers in developing better prevention measures.
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Affiliation(s)
- Cristian D Loaiza
- Center for Integrated BioSystems/Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, USA
| | - Naveen Duhan
- Center for Integrated BioSystems/Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, USA
| | - Matthew Lister
- Bioinformatics Facility, Center for Integrated BioSystems, Utah State University, USA
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate/Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322 USA
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Kalavi K, Jorjani O, Faghihi MA, Mowla SJ. Cytokine Gene Expression Alterations in Human Macrophages Infected by Leishmania major. CELL JOURNAL 2020; 22:476-481. [PMID: 32347041 PMCID: PMC7211285 DOI: 10.22074/cellj.2021.6524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 06/10/2019] [Indexed: 12/18/2022]
Abstract
Objective Leishmaniasis is caused by members of the Leishmania species and constitute a group of infective diseases that range from cutaneous lesions to lethal visceral forms. In infected persons, macrophages recognize and eliminate the parasites via phagocytosis. In order to change a hostile environment into an environment adequate for survival and reproduction, the engulfed Leishmania species needs to modulate the function of its host macrophage. The expression patterns of cytokine genes such as interleukin-12 (IL-12), tumour necrosis factor-alpha (TNF-α), IL-1, and interferon-gamma (IFNγ) represent the immune response. In this study, we employed an RNA-seq approach for human monocyte-derived macrophages infected with Leishmania major (L. major) to decipher cytokine gene expression alterations in host macrophages. Materials and Methods In this descriptive study, human monocytes were isolated by magnetic activated cell sorting (MACS) and cultured in the presence of monocyte colony stimulating factor (M-CSF) to obtain the macrophages. Monocyte-derived macrophages were then co-cultured with metacyclic promastigotes of L. major for 4 hours. RNA isolation was performed using TRIzol reagent. RNA sequencing was performed using the Illumina sequencing platforms. Gene expression analysis was performed using a Bioconductor DESeq2 package. Results Our data revealed significant changes in immune response gene expressions in macrophages infected with L. major, with an up-regulation of cytokines and mostly down-regulation of their receptors. Conclusion The obtained data could shed more light on the biology of L. major and how the host cell responds to leishmaniasis.
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Affiliation(s)
- Khodaberdi Kalavi
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.,Department of Laboratory Sciences, School of Allied Medical Sciences, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ogholniaz Jorjani
- Department of Laboratory Sciences, School of Allied Medical Sciences, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mohammad Ali Faghihi
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Psychiatry and Behavioral Sciences, School of Medicine, University of Miami, FL, USA
| | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran. Electronic Address:
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Coutinho-Abreu IV, Serafim TD, Meneses C, Kamhawi S, Oliveira F, Valenzuela JG. Distinct gene expression patterns in vector-residing Leishmania infantum identify parasite stage-enriched markers. PLoS Negl Trop Dis 2020; 14:e0008014. [PMID: 32126078 PMCID: PMC7053709 DOI: 10.1371/journal.pntd.0008014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/24/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Leishmaniasis is a vector-borne neglected disease. Inside the natural sand fly vector, the promastigote forms of Leishmania undergo a series of extracellular developmental stages to reach the infectious stage, the metacyclic promastigote. There is limited information regarding the expression profile of L. infantum developmental stages inside the sand fly vector, and molecular markers that can distinguish the different parasite stages are lacking. METHODOLOGY/PRINCIPAL FINDINGS We performed RNAseq on unaltered midguts of the sand fly Lutzomyia longipalpis after infection with L. infantum parasites. RNAseq was carried out at various time points throughout parasite development. Principal component analysis separated the transcripts corresponding to the different Leishmania promastigote stages, the procyclic, nectomonad, leptomonad and metacyclics. Importantly, there were a significant number of differentially expressed genes when comparing the sequential development of the various Leishmania stages in the sand fly. There were 836 differentially expressed (DE) genes between procyclic and long nectomonad promastigotes; 113 DE genes between nectomonad and leptomonad promastigotes; and 302 DE genes between leptomonad and metacyclic promastigotes. Most of the DE genes do not overlap across stages, highlighting the uniqueness of each Leishmania stage. Furthermore, the different stages of Leishmania parasites exhibited specific transcriptional enrichment across chromosomes. Using the transcriptional signatures exhibited by distinct Leishmania stages during their development in the sand fly midgut, we determined the genes predominantly enriched in each stage, identifying multiple potential stage-specific markers for L. infantum. CONCLUSIONS Overall, these findings demonstrate the transcriptional plasticity of the Leishmania parasite inside the sand fly vector and provide a repertoire of potential stage-specific markers for further development as molecular tools for epidemiological studies.
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Affiliation(s)
- Iliano V. Coutinho-Abreu
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Tiago D. Serafim
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Claudio Meneses
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Shaden Kamhawi
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Fabiano Oliveira
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Jesus G. Valenzuela
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
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Differential immune response modulation in early Leishmania amazonensis infection of BALB/c and C57BL/6 macrophages based on transcriptome profiles. Sci Rep 2019; 9:19841. [PMID: 31882833 PMCID: PMC6934472 DOI: 10.1038/s41598-019-56305-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 12/10/2019] [Indexed: 12/26/2022] Open
Abstract
The fate of Leishmania infection can be strongly influenced by the host genetic background. In this work, we describe gene expression modulation of the immune system based on dual global transcriptome profiles of bone marrow-derived macrophages (BMDMs) from BALB/c and C57BL/6 mice infected with Leishmania amazonensis. A total of 12,641 host transcripts were identified according to the alignment to the Mus musculus genome. Differentially expressed genes (DEGs) profiling revealed a differential modulation of the basal genetic background between the two hosts independent of L. amazonensis infection. In addition, in response to early L. amazonensis infection, 10 genes were modulated in infected BALB/c vs. non-infected BALB/c macrophages; and 127 genes were modulated in infected C57BL/6 vs. non-infected C57BL/6 macrophages. These modulated genes appeared to be related to the main immune response processes, such as recognition, antigen presentation, costimulation and proliferation. The distinct gene expression was correlated with the susceptibility and resistance to infection of each host. Furthermore, upon comparing the DEGs in BMDMs vs. peritoneal macrophages, we observed no differences in the gene expression patterns of Jun, Fcgr1 and Il1b, suggesting a similar activation trends of transcription factor binding, recognition and phagocytosis, as well as the proinflammatory cytokine production in response to early L. amazonensis infection. Analysis of the DEG profile of the parasite revealed only one DEG among the 8,282 transcripts, indicating that parasite gene expression in early infection does not depend on the host genetic background.
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36
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Smirlis D, Dingli F, Pescher P, Prina E, Loew D, Rachidi N, Späth GF. SILAC-based quantitative proteomics reveals pleiotropic, phenotypic modulation in primary murine macrophages infected with the protozoan pathogen Leishmania donovani. J Proteomics 2019; 213:103617. [PMID: 31846769 DOI: 10.1016/j.jprot.2019.103617] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/04/2019] [Accepted: 12/13/2019] [Indexed: 01/06/2023]
Abstract
Leishmaniases are major vector-borne tropical diseases responsible for great human morbidity and mortality, caused by protozoan, trypanosomatid parasites of the genus Leishmania. In the mammalian host, parasites survive and multiply within mononuclear phagocytes, especially macrophages. However, the underlying mechanisms by which Leishmania spp. affect their host are not fully understood. Herein, proteomic alterations of primary, bone marrow-derived BALB/c macrophages are documented after 72 h of infection with Leishmania donovani insect-stage promastigotes, applying a SILAC-based, quantitative proteomics approach. The protocol was optimised by combining strong anion exchange and gel electrophoresis fractionation that displayed similar depth of analysis (combined total of 6189 mouse proteins). Our analyses revealed 86 differentially modulated proteins (35 showing increased and 51 decreased abundance) in response to Leishmania donovani infection. The proteomics results were validated by analysing the abundance of selected proteins. Intracellular Leishmania donovani infection led to changes in various host cell biological processes, including primary metabolism and catabolic process, with a significant enrichment in lysosomal organisation. Overall, our analysis establishes the first proteome of bona fide primary macrophages infected ex vivo with Leishmania donovani, revealing new mechanisms acting at the host/pathogen interface. SIGNIFICANCE: Little is known on proteome changes that occur in primary macrophages after Leishmania donovani infection. This study describes a SILAC-based quantitative proteomics approach to characterise changes of bone marrow-derived macrophages infected with L. donovani promastigotes for 72 h. With the application of SILAC and the use of SAX and GEL fractionation methods, we have tested new routes for proteome quantification of primary macrophages. The protocols developed here can be applicable to other diseases and pathologies. Moreover, this study sheds important new light on the "proteomic reprogramming" of infected macrophages in response to L. donovani promastigotes that affects primary metabolism, cellular catabolic processes, and lysosomal/vacuole organisation. Thus, our study reveals key molecules and processes that act at the host/pathogen interface that may inform on new immuno- or chemotherapeutic interventions to combat leishmaniasis.
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Affiliation(s)
- Despina Smirlis
- Institut Pasteur and Institut National de Santé et Recherche Médicale INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France; Hellenic Pasteur Institute, Molecular Parasitology Laboratory, Athens, Greece.
| | - Florent Dingli
- Laboratoire de Spectrométrie de Masse Protéomique, Centre de Recherche, Institut Curie, Université de recherche PSL, Paris, France
| | - Pascale Pescher
- Institut Pasteur and Institut National de Santé et Recherche Médicale INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | - Eric Prina
- Institut Pasteur and Institut National de Santé et Recherche Médicale INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique, Centre de Recherche, Institut Curie, Université de recherche PSL, Paris, France
| | - Najma Rachidi
- Institut Pasteur and Institut National de Santé et Recherche Médicale INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | - Gerald F Späth
- Institut Pasteur and Institut National de Santé et Recherche Médicale INSERM U1201, Unité de Parasitologie Moléculaire et Signalisation, Paris, France.
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Metabolomic Profile of BALB/c Macrophages Infected with Leishmania amazonensis: Deciphering L-Arginine Metabolism. Int J Mol Sci 2019; 20:ijms20246248. [PMID: 31835767 PMCID: PMC6940984 DOI: 10.3390/ijms20246248] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/06/2019] [Accepted: 12/08/2019] [Indexed: 12/18/2022] Open
Abstract
Background: Leishmaniases are neglected tropical diseases that are caused by Leishmania, being endemic worldwide. L-arginine is an essential amino acid that is required for polyamines production on mammal cells. During Leishmania infection of macrophages, L-arginine is used by host and parasite arginase to produce polyamines, leading to parasite survival; or, by nitric oxide synthase 2 to produce nitric oxide leading to parasite killing. Here, we determined the metabolomic profile of BALB/c macrophages that were infected with L. amazonensis wild type or with L. amazonensis arginase knockout, correlating the regulation of L-arginine metabolism from both host and parasite. Methods: The metabolites of infected macrophages were analyzed by capillary electrophoresis coupled with mass spectrometry (CE-MS). The metabolic fingerprints analysis provided the dual profile from the host and parasite. Results: We observed increased levels of proline, glutamic acid, glutamine, L-arginine, ornithine, and putrescine in infected-L. amazonensis wild type macrophages, which indicated that this infection induces the polyamine production. Despite this, we observed reduced levels of ornithine, proline, and trypanothione in infected-L. amazonensis arginase knockout macrophages, indicating that this infection reduces the polyamine production. Conclusions: The metabolome fingerprint indicated that Leishmania infection alters the L-arginine/polyamines/trypanothione metabolism inside the host cell and the parasite arginase impacts on L-arginine metabolism and polyamine production, defining the infection fate.
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Cruz AK, Freitas-Castro F. Genome and transcriptome analyses of Leishmania spp.: opening Pandora's box. Curr Opin Microbiol 2019; 52:64-69. [PMID: 31212190 DOI: 10.1016/j.mib.2019.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 05/13/2019] [Indexed: 01/07/2023]
Abstract
In the last 30 years, significant advances in genetic manipulation tools along with complete genome and transcriptome sequencing have advanced our understanding of the biology of Leishmania parasites and their interplay with the sand fly and mammalian hosts. High-throughput sequencing in association with CRISPR/Cas9 have prepared the ground for significant advances. Given the richness of the progress made over the last decade, in this article, we focused on the most recent contributions of genome-wide and transcriptome analyses of Leishmania spp., which permit the comparison of life cycle stages, the evaluation of different strains and species in their natural niches and in the field and the simultaneously comparison of the gene expression profiles of parasites and hosts.
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Affiliation(s)
- Angela Kaysel Cruz
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
| | - Felipe Freitas-Castro
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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39
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Fernandes JCR, Aoki JI, Maia Acuña S, Zampieri RA, Markus RP, Floeter-Winter LM, Muxel SM. Melatonin and Leishmania amazonensis Infection Altered miR-294, miR-30e, and miR-302d Impacting on Tnf, Mcp-1, and Nos2 Expression. Front Cell Infect Microbiol 2019; 9:60. [PMID: 30949455 PMCID: PMC6435487 DOI: 10.3389/fcimb.2019.00060] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/27/2019] [Indexed: 12/13/2022] Open
Abstract
Leishmaniases are neglected diseases that cause a large spectrum of clinical manifestations, from cutaneous to visceral lesions. The initial steps of the inflammatory response involve the phagocytosis of Leishmania and the parasite replication inside the macrophage phagolysosome. Melatonin, the darkness-signaling hormone, is involved in modulation of macrophage activation during infectious diseases, controlling the inflammatory response against parasites. In this work, we showed that exogenous melatonin treatment of BALB/c macrophages reduced Leishmania amazonensis infection and modulated host microRNA (miRNA) expression profile, as well as cytokine production such as IL-6, MCP-1/CCL2, and, RANTES/CCL9. The role of one of the regulated miRNA (miR-294-3p) in L. amazonensis BALB/c infection was confirmed with miRNA inhibition assays, which led to increased expression levels of Tnf and Mcp-1/Ccl2 and diminished infectivity. Additionally, melatonin treatment or miR-30e-5p and miR-302d-3p inhibition increased nitric oxide synthase 2 (Nos2) mRNA expression levels and nitric oxide (NO) production, altering the macrophage activation state and reducing infection. Altogether, these data demonstrated the impact of melatonin treatment on the miRNA profile of BALB/c macrophage infected with L. amazonensis defining the infection outcome.
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Affiliation(s)
- Juliane Cristina Ribeiro Fernandes
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, Brazil
| | - Juliana Ide Aoki
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Stephanie Maia Acuña
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Ricardo Andrade Zampieri
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Regina P Markus
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | - Sandra Marcia Muxel
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Rosani U, Young T, Bai CM, Alfaro AC, Venier P. Dual Analysis of Virus-Host Interactions: The Case of Ostreid herpesvirus 1 and the Cupped Oyster Crassostrea gigas. Evol Bioinform Online 2019; 15:1176934319831305. [PMID: 30828244 PMCID: PMC6388457 DOI: 10.1177/1176934319831305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/14/2019] [Indexed: 12/20/2022] Open
Abstract
Dual analyses of the interactions between Ostreid herpesvirus 1 (OsHV-1) and the bivalve Crassostrea gigas during infection can unveil events critical to the onset and progression of this viral disease and can provide novel strategies for mitigating and preventing oyster mortality. Among the currently used “omics” technologies, dual transcriptomics (dual RNA-seq) coupled with the analysis of viral DNA in the host tissues has greatly advanced the knowledge of genes and pathways mostly contributing to host defense responses, expression profiles of annotated and unknown OsHV-1 open reading frames (ORFs), and viral genome variability. In addition to dual RNA-seq, proteomics and metabolomics analyses have the potential to add complementary information, needed to understand how a malacoherpesvirus can redirect and exploit the vital processes of its host. This review explores our current knowledge of “omics” technologies in the study of host-pathogen interactions and highlights relevant applications of these fields of expertise to the complex case of C gigas infections by OsHV-1, which currently threaten the mollusk production sector worldwide.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, Padova, Italy
| | - Tim Young
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Chang-Ming Bai
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Paola Venier
- Department of Biology, University of Padova, Padova, Italy
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Ruy PDC, Monteiro-Teles NM, Miserani Magalhães RD, Freitas-Castro F, Dias L, Aquino Defina TP, Rosas De Vasconcelos EJ, Myler PJ, Kaysel Cruz A. Comparative transcriptomics in Leishmania braziliensis: disclosing differential gene expression of coding and putative noncoding RNAs across developmental stages. RNA Biol 2019; 16:639-660. [PMID: 30689499 DOI: 10.1080/15476286.2019.1574161] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Leishmaniasis is a worldwide public health problem caused by protozoan parasites of the genus Leishmania. Leishmania braziliensis is the most important species responsible for tegumentary leishmaniases in Brazil. An understanding of the molecular mechanisms underlying the success of this parasite is urgently needed. An in-depth study on the modulation of gene expression across the life cycle stages of L. braziliensis covering coding and noncoding RNAs (ncRNAs) was missing and is presented herein. Analyses of differentially expressed (DE) genes revealed that most prominent differences were observed between the transcriptomes of insect and mammalian proliferative forms (6,576 genes). Gene ontology (GO) analysis indicated stage-specific enriched biological processes. A computational pipeline and 5 ncRNA predictors allowed the identification of 11,372 putative ncRNAs. Most of the DE ncRNAs were found between the transcriptomes of insect and mammalian proliferative stages (38%). Of the DE ncRNAs, 295 were DE in all three stages and displayed a wide range of lengths, chromosomal distributions and locations; many of them had a distinct expression profile compared to that of their protein-coding neighbors. Thirty-five putative ncRNAs were submitted to northern blotting analysis, and one or more hybridization-positive signals were observed in 22 of these ncRNAs. This work presents an overview of the L. braziliensis transcriptome and its adjustments throughout development. In addition to determining the general features of the transcriptome at each life stage and the profile of protein-coding transcripts, we identified and characterized a variety of noncoding transcripts. The novel putative ncRNAs uncovered in L. braziliensis might be regulatory elements to be further investigated.
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Affiliation(s)
- Patrícia De Cássia Ruy
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Natália Melquie Monteiro-Teles
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Rubens Daniel Miserani Magalhães
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Felipe Freitas-Castro
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Leandro Dias
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | - Tania Paula Aquino Defina
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
| | | | - Peter J Myler
- b Center for Infectious Disease Research , Seattle, Washington , USA
| | - Angela Kaysel Cruz
- a Cell and Molecular Biology Department, Ribeirão Preto Medical School , University of São Paulo, Ribeirão Preto , São Paulo , Brazil
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Stamper BD, Davis M, Scott-Collins S, Tran J, Ton C, Simidyan A, Roberts SC. Model-based Evaluation of Gene Expression Changes in Response to Leishmania Infection. GENE REGULATION AND SYSTEMS BIOLOGY 2019; 13:1177625019828350. [PMID: 30792575 PMCID: PMC6376507 DOI: 10.1177/1177625019828350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/21/2018] [Indexed: 12/16/2022]
Abstract
Since the development of high-density microarray technology in the late 1990s, global host gene expression changes in response to various stimuli have been extensively studied. More than a dozen peer-reviewed publications have investigated the effect of Leishmania infection in various models since 2001. This review covers the transcriptional changes in macrophage models induced by various Leishmania species and summarizes the resulting impact these studies have on our understanding of the host response to leishmaniasis in vitro. Characterization of the similarities and differences between various model systems will not only further our understanding of Leishmania-induced changes to macrophage gene expression but also identify potential therapeutic targets in the future.
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Affiliation(s)
| | - Madison Davis
- School of Pharmacy, Pacific University Oregon, Hillsboro, OR, USA
| | | | - Julie Tran
- School of Pharmacy, Pacific University Oregon, Hillsboro, OR, USA
| | - Caryn Ton
- School of Pharmacy, Pacific University Oregon, Hillsboro, OR, USA
| | - Agapi Simidyan
- School of Pharmacy, Pacific University Oregon, Hillsboro, OR, USA
| | - Sigrid C Roberts
- School of Pharmacy, Pacific University Oregon, Hillsboro, OR, USA
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Shadab M, Das S, Banerjee A, Sinha R, Asad M, Kamran M, Maji M, Jha B, Deepthi M, Kumar M, Tripathi A, Kumar B, Chakrabarti S, Ali N. RNA-Seq Revealed Expression of Many Novel Genes Associated With Leishmania donovani Persistence and Clearance in the Host Macrophage. Front Cell Infect Microbiol 2019; 9:17. [PMID: 30805314 PMCID: PMC6370631 DOI: 10.3389/fcimb.2019.00017] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/17/2019] [Indexed: 12/14/2022] Open
Abstract
Host- as well as parasite-specific factors are equally crucial in allowing either the Leishmania parasites to dominate, or host macrophages to resist infection. To identify such factors, we infected murine peritoneal macrophages with either the virulent (vAG83) or the non-virulent (nvAG83) parasites of L. donovani. Then, through dual RNA-seq, we simultaneously elucidated the transcriptomic changes occurring both in the host and the parasites. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the differentially expressed (DE) genes, we showed that the vAG83-infected macrophages exhibit biased anti-inflammatory responses compared to the macrophages infected with the nvAG83. Moreover, the vAG83-infected macrophages displayed suppression of many important cellular processes, including protein synthesis. Further, through protein-protein interaction study, we showed significant downregulation in the expression of many hubs and hub-bottleneck genes in macrophages infected with vAG83 as compared to nvAG83. Cell signaling study showed that these two parasites activated the MAPK and PI3K-AKT signaling pathways differentially in the host cells. Through gene ontology analyses of the parasite-specific genes, we discovered that the genes for virulent factors and parasite survival were significantly upregulated in the intracellular amastigotes of vAG83. In contrast, genes involved in the immune stimulations, and those involved in negative regulation of the cell cycle and transcriptional regulation, were upregulated in the nvAG83. Collectively, these results depicted a differential regulation in the host and the parasite-specific molecules during in vitro persistence and clearance of the parasites.
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Affiliation(s)
- Mohammad Shadab
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Sonali Das
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Anindyajit Banerjee
- Structural Biology and Bio-Informatics Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Roma Sinha
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Mohammad Asad
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Mohd Kamran
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Mithun Maji
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Baijayanti Jha
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Makaraju Deepthi
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, India
| | | | | | - Bipin Kumar
- Nucleome Informatics Pvt. Ltd., Hyderabad, India
| | - Saikat Chakrabarti
- Structural Biology and Bio-Informatics Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Nahid Ali
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, India
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LaMonte GM, Orjuela-Sanchez P, Calla J, Wang LT, Li S, Swann J, Cowell AN, Zou BY, Abdel-Haleem Mohamed AM, Villa Galarce ZH, Moreno M, Tong Rios C, Vinetz JM, Lewis N, Winzeler EA. Dual RNA-seq identifies human mucosal immunity protein Mucin-13 as a hallmark of Plasmodium exoerythrocytic infection. Nat Commun 2019; 10:488. [PMID: 30700707 PMCID: PMC6353872 DOI: 10.1038/s41467-019-08349-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 12/24/2018] [Indexed: 12/28/2022] Open
Abstract
The exoerythrocytic stage of Plasmodium infection is a critical window for prophylactic intervention. Using genome-wide dual RNA sequencing of flow-sorted infected and uninfected hepatoma cells we show that the human mucosal immunity gene, mucin-13 (MUC13), is strongly upregulated during Plasmodium exoerythrocytic hepatic-stage infection. We confirm MUC13 transcript increases in hepatoma cell lines and primary hepatocytes. In immunofluorescence assays, host MUC13 protein expression distinguishes infected cells from adjacent uninfected cells and shows similar colocalization with parasite biomarkers such as UIS4 and HSP70. We further show that localization patterns are species independent, marking both P. berghei and P. vivax infected cells, and that MUC13 can be used to identify compounds that inhibit parasite replication in hepatocytes. This data provides insights into host-parasite interactions in Plasmodium infection, and demonstrates that a component of host mucosal immunity is reprogrammed during the progression of infection.
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Affiliation(s)
- Gregory M LaMonte
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Pamela Orjuela-Sanchez
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Jaeson Calla
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Lawrence T Wang
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Shangzhong Li
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Justine Swann
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Annie N Cowell
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bing Yu Zou
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
| | - Alyaa M Abdel-Haleem Mohamed
- Computational Bioscience Research Centre (CBRC) and Biological and Environmental Sciences and Engineering (BESE) division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Zaira Hellen Villa Galarce
- Laboratorio ICEMR-Amazonia, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Marta Moreno
- Laboratorio ICEMR-Amazonia, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- London School of Hygiene and Tropical Medicine, Department of Immunology and Infection, London, UK
| | - Carlos Tong Rios
- Laboratorio ICEMR-Amazonia, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joseph M Vinetz
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Laboratorio ICEMR-Amazonia, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
- Yale School of Medicine, Section of Infectious Diseases, Department of Internal Medicine, New Haven, CT, USA
| | - Nathan Lewis
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA.
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45
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Inbred mouse strains differentially susceptible to Leishmania donovani infection differ in their immune cell metabolism. Cytokine 2018; 112:12-15. [DOI: 10.1016/j.cyto.2018.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/31/2018] [Accepted: 06/02/2018] [Indexed: 11/21/2022]
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Muxel SM, Acuña SM, Aoki JI, Zampieri RA, Floeter-Winter LM. Toll-Like Receptor and miRNA-let-7e Expression Alter the Inflammatory Response in Leishmania amazonensis-Infected Macrophages. Front Immunol 2018; 9:2792. [PMID: 30555476 PMCID: PMC6283264 DOI: 10.3389/fimmu.2018.02792] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022] Open
Abstract
Parasite recognition by Toll-like receptors (TLRs) contributes to macrophage activation and subsequent control of Leishmania infection through the coordinated production of pro-inflammatory and microbicidal effector molecules. The modulation of microRNA (miRNA) expression by Leishmania infection potentially mediates the post-transcriptional regulation of the expression of genes involved in leishmanicidal activity. Here, the contribution of TLR signaling to the miRNA profile and gene expression was evaluated in Leishmania amazonensis-infected murine macrophages. The infectivity of L. amazonensis was higher in murine bone marrow-derived macrophages from mice knockout for myeloid differentiation factor 88 (MyD88−/−), TLR2 (TLR2−/−), or TLR4 (TLR4−/−) than wild type C57BL/6 (WT). L. amazonensis infection of WT macrophages modulated the expression of 32% of the miRNAs analyzed, while 50% were upregulated. The absence of MyD88, TLR2, and TLR4 altered the percentage of miRNAs modulated during L. amazonensis infection, including the downregulation of let-7e expression. Moreover, the absence of signals mediated by MyD88, TLR2, or TLR4 reduced nitric oxide synthase 2 (Nos2) mRNA expression during infection. Indeed, the inhibition of let-7e increased levels of the Nos2 mRNA and NOS2 (or iNOS) protein and nitric oxide (NO) production in L. amazonensis-infected macrophages (4–24 h). The absence of TLR2 and inhibition of let-7e increased the expression of the arginase 1 (Arg1) mRNA but did not alter the protein level during infection. However, higher levels of the L-arginine transporters Cat2B and Cat1 were detected in the absence of Myd88 signaling during infection but were not altered following let-7e inhibition. The inhibition of let-7e impacted the global expression of genes in the TLR pathway by upregulating the expression of recognition and adaptors molecules, such as Tlr6, Tlr9, Ly96, Tirap, Traf 6, Ticam1, Tollip, Casp8, Map3k1, Mapk8, Nfkbib, Nfkbil1, Ppara, Mapk8ip3, Hspd1, and Ube2n, as well as immunomodulators, such as Ptgs2/Cox2, Csf 2, Csf 3, Ifnb1, Il6ra, and Ilr1, impacting NOS2 expression, NO production and parasite infectiveness. In conclusion, L. amazonensis infection alters the TLR signaling pathways by modulating the expression of miRNAs in macrophages to subvert the host immune responses.
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Affiliation(s)
- Sandra Marcia Muxel
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Stephanie Maia Acuña
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Juliana Ide Aoki
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Ricardo Andrade Zampieri
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Frönicke L, Bronner DN, Byndloss MX, McLaughlin B, Bäumler AJ, Westermann AJ. Toward Cell Type-Specific In Vivo Dual RNA-Seq. Methods Enzymol 2018; 612:505-522. [PMID: 30502956 DOI: 10.1016/bs.mie.2018.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Dual RNA-seq has emerged as a genome-wide expression profiling technique, simultaneously measuring RNA transcript levels in a given host and its pathogen during an infection. Recently, the method was transferred from cell culture to in vivo models of bacterial infections; however, specific host cell-type resolution has not yet been achieved. Here we present a detailed protocol that describes the application of Dual RNA-seq to murine colonocytes isolated from mice infected with the enteric pathogen Salmonella Typhimurium. At day 5 after oral infection, the mice were humanely euthanized, their colons extracted, and colonocytes isolated and fixed. Upon antibody staining of cell type-specific surface markers, the fraction of Salmonella-invaded colonocytes was collected by fluorescence-activated cell sorting based on a fluorescent signal emitted by the internalized bacteria. Total RNA was extracted from cells enriched by this method, and ribosomal transcripts from host and microbial cells were removed prior to cDNA synthesis and library generation. We compared different protocols for library preparation and discuss their respective advantages and caveats when applied to minute RNA amounts that constitute an inherent challenge for in vivo transcriptomics. Our results introduce an ultralow input protocol that holds promise for cell type-specific in vivo Dual RNA-seq for charting gene expression of a bacterial pathogen within its respective in vivo niche, along with the consequent host response.
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Affiliation(s)
- Lutz Frönicke
- University of California Davis Genome Center, Davis, CA, United States
| | - Denise N Bronner
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, United States
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, United States
| | - Bridget McLaughlin
- Comprehensive Cancer Center Flow Cytometry Shared Resource, University of California Davis, Davis, CA, United States
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, United States
| | - Alexander J Westermann
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-Based Infection Research (HIRI), Würzburg, Germany.
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48
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Veras PST, Ramos PIP, de Menezes JPB. In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected Macrophages. Front Cell Infect Microbiol 2018; 8:326. [PMID: 30283744 PMCID: PMC6157484 DOI: 10.3389/fcimb.2018.00326] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/27/2018] [Indexed: 12/12/2022] Open
Abstract
Leishmaniasis is a vector-borne, neglected tropical disease with a worldwide distribution that can present in a variety of clinical forms, depending on the parasite species and host genetic background. The pathogenesis of this disease remains far from being elucidated because the involvement of a complex immune response orchestrated by host cells significantly affects the clinical outcome. Among these cells, macrophages are the main host cells, produce cytokines and chemokines, thereby triggering events that contribute to the mediation of the host immune response and, subsequently, to the establishment of infection or, alternatively, disease control. There has been relatively limited commercial interest in developing new pharmaceutical compounds to treat leishmaniasis. Moreover, advances in the understanding of the underlying biology of Leishmania spp. have not translated into the development of effective new chemotherapeutic compounds. As a result, biomarkers as surrogate disease endpoints present several potential advantages to be used in the identification of targets capable of facilitating therapeutic interventions considered to ameliorate disease outcome. More recently, large-scale genomic and proteomic analyses have allowed the identification and characterization of the pathways involved in the infection process in both parasites and the host, and these analyses have been shown to be more effective than studying individual molecules to elucidate disease pathogenesis. RNA-seq and proteomics are large-scale approaches that characterize genes or proteins in a given cell line, tissue, or organism to provide a global and more integrated view of the myriad biological processes that occur within a cell than focusing on an individual gene or protein. Bioinformatics provides us with the means to computationally analyze and integrate the large volumes of data generated by high-throughput sequencing approaches. The integration of genomic expression and proteomic data offers a rich multi-dimensional analysis, despite the inherent technical and statistical challenges. We propose that these types of global analyses facilitate the identification, among a large number of genes and proteins, those that hold potential as biomarkers. The present review focuses on large-scale studies that have identified and evaluated relevant biomarkers in macrophages in response to Leishmania infection.
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Affiliation(s)
- Patricia Sampaio Tavares Veras
- Laboratory of Host-Parasite Interaction and Epidemiology, Gonçalo Moniz Institute, Fiocruz-Bahia, Salvador, Brazil.,National Institute of Tropical Disease, Brasilia, Brazil
| | - Pablo Ivan Pereira Ramos
- Center for Data and Knowledge Integration for Health, Gonçalo Moniz Institute, Fiocruz-Bahia, Salvador, Brazil
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Ontoria E, Hernández-Santana YE, González-García AC, López MC, Valladares B, Carmelo E. Transcriptional Profiling of Immune-Related Genes in Leishmania infantum-Infected Mice: Identification of Potential Biomarkers of Infection and Progression of Disease. Front Cell Infect Microbiol 2018; 8:197. [PMID: 30013952 PMCID: PMC6036295 DOI: 10.3389/fcimb.2018.00197] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/28/2018] [Indexed: 12/27/2022] Open
Abstract
Leishmania spp. is a protozoan parasite that affects millions of people around the world. At present, there is no effective vaccine to prevent leishmaniases in humans. A major limitation in vaccine development is the lack of precise understanding of the particular immunological mechanisms that allow parasite survival in the host. The parasite-host cell interaction induces dramatic changes in transcriptome patterns in both organisms, therefore, a detailed analysis of gene expression in infected tissues will contribute to the evaluation of drug and vaccine candidates, the identification of potential biomarkers, and the understanding of the immunological pathways that lead to protection or progression of disease. In this large-scale analysis, differential expression of 112 immune-related genes has been analyzed using high-throughput qPCR in spleens of infected and naïve Balb/c mice at four different time points. This analysis revealed that early response against Leishmania infection is characterized by the upregulation of Th1 markers and M1-macrophage activation molecules such as Ifng, Stat1, Cxcl9, Cxcl10, Ccr5, Cxcr3, Xcl1, and Ccl3. This activation doesn't protect spleen from infection, since parasitic burden rises along time. This marked difference in gene expression between infected and control mice disappears during intermediate stages of infection, probably related to the strong anti-inflammatory and immunosuppresory signals that are activated early upon infection (Ctla4) or remain activated throughout the experiment (Il18bp). The overexpression of these Th1/M1 markers is restored later in the chronic phase (8 wpi), suggesting the generation of a classical "protective response" against leishmaniasis. Nonetheless, the parasitic burden rockets at this timepoint. This apparent contradiction can be explained by the generation of a regulatory immune response characterized by overexpression of Ifng, Tnfa, Il10, and downregulation Il4 that counteracts the Th1/M1 response. This large pool of data was also used to identify potential biomarkers of infection and parasitic burden in spleen, on the bases of two different regression models. Given the results, gene expression signature analysis appears as a useful tool to identify mechanisms involved in disease outcome and to establish a rational approach for the identification of potential biomarkers useful for monitoring disease progression, new therapies or vaccine development.
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Affiliation(s)
- Eduardo Ontoria
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Spain
| | - Yasmina E. Hernández-Santana
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Spain
| | - Ana C. González-García
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Spain
| | - Manuel C. López
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Basilio Valladares
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Spain
| | - Emma Carmelo
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Spain
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50
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Soni B, Saha B, Singh S. Systems cues governing IL6 signaling in leishmaniasis. Cytokine 2018; 106:169-175. [DOI: 10.1016/j.cyto.2017.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/30/2017] [Accepted: 11/02/2017] [Indexed: 12/18/2022]
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